Mod Organizer

[bob11]

Yeah I loaded some mods I don't have the DLC for and they are in the right plugin list and uncheck ok, but got no idea how toremove them because the aren't in the left list, maybe they are the mods that were installed by NMM. Would that be the reason?

 

Yeah.  MO can see the .esps cause they are THERE, in the Data folder, but since it's installed through NMM, it can't do anything with their assets being there.  If the mods installed through NMM are NOT replacers, disabling just the .esp will do the trick.  If it replaces stuff like meshes or textures besides other stuff, you either need to uninstall it through NMM and pray, or manually uninstall it and pray again (you know, that you didn't erase something you wanted by change).

 

Not sure how importing from NMM works, I just reinstalled the game after I got fed up with NMM and used MO on a clean game.

[RitualClarity]

@ Halstrom

You will have some data that gets in the "overwrite" folder on the left side after you start playing a game. The data from the NVSE Extender 12. I have experimented and believe it would be safe to create a "SAVE NVSE Extender" using the "create mod" option if you need to keep or clean the overwrite folder. Then when you change games (since NVSE Extender Saves are game specific that is that character you created or saves created with that game play) you can click on the Mod you created that has the saves in them. Oh replace SAVE with the name of the profile. Seems to work well so far haven't been able to test it fully because I ended up having a strange .ini issue where one of the mods wouldn't release and show up in MO. Might have been a mistake when using FOMM at the same time (through MO only of course).

[AwfulArchdemon]

 

 

I like fixing bugs however I don't want to add issues to the game with mods. either. However I guess with MO it don't matter that much. I can load up the mods and the patches and just click and play with various load orders until I find the combination that I like. Just with Skyrim's dam persistent save data it makes it much more likely that I will leave remnants of any changes in the file even after I test so I would have to start from a truly "clean save" point at various points in the game. (clean no mods game only) Then I can jump in to various locations and tests and be able to thoroughly test various combinations with the save import option that MO has.

 

Good that I belong to this community... LOL. I could always post the load orders and ask for suggestions when I start getting a little more complex load orders. Right now I am running (if I run) a plain game. I don't even have MO setup at this point. Had some issues with the OS and such. Working on getting some upgrades and cleanups then I should be able to dedicate some space (machine possibly) to just gaming fun. Then I can keep working on a single game play and add mods and archive and all sorts of things that I wanted to do. Perhaps even start to some light modding. Already got some ideas. Just dreams, thoughts and aspirations. I won't know how much or how quickly I can progress through those idea or even if they are good.

 

 

Oh good question. How to you export the load order from MO? I have loaded mods. Got FINIS to work, imported and created a variety of characters (at one time one of each race and sex). but never figured out how to export the load orders or get the papyrus records. (stuff I would need if I every wanted suggestions or tech support beyond basic installation)

Sorry RC. I had issues posting. Had to squash a bug. It's dead now.

 

If you want your mod order to stay the same, just move your profiles folders over to the new version. In those profile folders you have a loadorder.txt and a modlist.txt. The loadorder.txt tells MO which order the mods should be in, and the modlist.txt tells MO which mods to activate. I added my profiles and mods folders before I even fired up the new version, since those folders don't exist right out of the zip.

 

Loving the new look! (yay HeavyDude!)

[RitualClarity]

 

If you want your mod order to stay the same, just move your profiles folders over to the new version. In those profile folders you have a loadorder.txt and a modlist.txt. The loadorder.txt tells MO which order the mods should be in, and the modlist.txt tells MO which mods to activate. I added my profiles and mods folders before I even fired up the new version, since those folders don't exist right out of the zip.

 

Loving the new look! (yay HeavyDude!)

 

 

So if I just wanted the load order all I would have to do is open the profiles folder and copy that loadorder.txt. Then I can past it here or elsewhere to find if I have a load order issue. Correct..

 

Anyway thanks for the answer you gave me even though it wasnt what i needed to know I still learned something cool anyway. I never thought of using the loadorder.txt and modlist.txt to be able to transfer the info from one MO to another.

 

In a way someone can download the entire mod library of selected mods, set up the game, then just export those two files to people and their game would be already set up... Provided they can put them back into the correct place... lol.

 

 

[Rabblerouser]

Is HDT impossible with MO considering you need use use NifSkope for it.

NifSkope doesn't seem to like MO. MO seems to crash in the background when NifSkope is run through MO.

[AwfulArchdemon]

Yeah, the nifskope thing isn't really feasible right now. Maybe soon. Not sure yet.

[Rabblerouser]

Yeah, the nifskope thing isn't really feasible right now. Maybe soon. Not sure yet.

So HDT is impossible through MO?

[bob11]

 

Yeah, the nifskope thing isn't really feasible right now. Maybe soon. Not sure yet.

So HDT is impossible through MO?

 

 

Why is HDT impossible through MO? It works normally here.

[AwfulArchdemon]

 

Yeah, the nifskope thing isn't really feasible right now. Maybe soon. Not sure yet.

So HDT is impossible through MO?

 

I don't use it, but I'm checking it out now. Are we talking about the same thing? You say you need to keep NifSkope running through MO to use it? I must be missing something here. From looking at the files, I'd say there's no reason it wouldn't work...

[judge0]

Is HDT impossible with MO considering you need use use NifSkope for it.

NifSkope doesn't seem to like MO. MO seems to crash in the background when NifSkope is run through MO.

NifSkope does not recognize symbolic links and junctions in the file system, hence it is flaky under MO

 

Neither the High Heels system or Physics engine HDT are dependent on NifSkope running.

 

Both High heels and HDT Physics work under MO.

 

If you mean making changes to HDT settings on meshes, you will have to work "blind"

 

That is, if you refer to a texture or a script, you have to refer to it as if all the files were installed under the Skyrim\Data folder. Needless to say, but if you are trying to use NifSkope to browse to the files location, it won't work.

[Terriblypleased]

So I'm trying to sort out MO but keep getting issues.

I have a bunch of flags I'm uncertain what to do with.

 

-Overwrites files

-Overwriten files

 

and the ones that are the most frustrating 

 

-No valid game data

 

No some ones told me that the overwrites and overwritten can be solved by changing the load order? Is this correct?

 

For the "No valid game data" it's slightly more frustrating.

 

"""First time you open such a mod MO mentions 'no valid game data' and gives you a help tour what it means and how to correct it. Select data directory, right click and select 'set data directory'. Now MO point to the data directory and tells you 'looks good'. BUT before doing so move with drag/drop readme.txt first to data directory because else its lost. Of course with 'unset data directory'you can undo it. I like my mods neatly arranged. I always select manual create a Docs/<modname> at the same lvl as for example textures/meshes and put readme's or example jpg files there.""

 

Now I didn't get a tour and I double clicked the mod inside MO and the data folders I've found in branched directories there don't give me an option of "set data directory" when I right click them. So confused.

 

SO I guess my questions are:

1) Do I repeatedly shuffle around files that have "Overwritten" and "overwrites" ?

2) What the heck do I do with the "No valid game data" ?

 

Oh and I suppose:

3)  Where do I go to change load order? Is it the left window under profile? Or is it the one in the plug in tab on the right?

 

Ta!

[Uhuru N'Uru]

First I have Made a post before about this but new changes have occurred.

Mod Organizer Official Support Forums are now part of STEP Forums where Tannin the Author has control of content and it is run independant of STEP, in theory. Although in practice it is more like a collaboration as STEP have changed their official sanctioned manager from Wrye Bash to Mod Organizer.

The contributers to STEP are some of the most scientific modders out there. They test by rigourous means and were the ones who found the 3.1 GB engine limit also Sheson ended up relying on their Testing methods to push his Memory Fix to the limits as though many pushed things they actually tested it.

This was after he announced his fix on ENB site not before, the fix itself is all Sheson's.

 

So their help and advice is a boost to Mod Organizer Support, The Wiki Guide on STEP is Official Mod Organizer Documentation so all in one support available with full Subforum makes it much better than Nexus one thead system.

 

Mod Organizer Official Support Forums

 

Right so now to repeat some of what's posted there

 

No Valid Game Data

This simply means no ESP's/ESM's and/or Meshes and/or Textures etc are in the archive or Game Data. Stuff the Game uses with most mods and hence Valid Game Data.

BodySlide 2 Settings files will produce this warning. also the SkSE data files which are just scripts and many SkSE Plugins which are usually DLL's and again not game Data.

 

Mod Organizer warnings are all like this, it's saying that's unusual, are you sure you are doing this right?

Not because it thinks you are not, but because it doesn't think at all.

So it is alerting the modder just in case something is wrong.

You are then informed and can say everythings OK, in this case I'm adding Modding files, not game Data

or

Rarely, if game data should be present, this lets you put it right before the crashes start.

 

Overwrite Folder

This one gives modders a lot of trouble so no surprise you are puzzled. Basically Overwite is a Temparary working folder and most of the time you don't see this used at all but any time you update mods it is used and emptied when that use is done it's the backup folder as when Mods are changed always copy and then move is used.

 

If Mod Organizer did not use 3rd Party software nothing would ever be left here. When it is it's because Mod Organizer has no way to know where to put the files or the program involved would create a new file or folder normally in Data folder, separate from normal Mods like TES5Edit Backups or Bashed Patch, FNIS also does this.

 

Telling you when this happens is asking for your orders usually just move to correct mod or create new mod.

The main thing to be aware of is there is only one Overwrite Folder for all profiles and it has last priority whatever is there will win all conflicts so not good to leave anything in it even bashed patch should be made into a mod of for each profile. See STEP for greater details as this is just basics.

 

Do not confuse

• The Overwrite Folder above (which is always Last in Priority listing and never actually given a priority Number)
• Overwrites and Overwritten Flags which indicates individual files conflicts and which wins or Overwrites and which loses or is Overwritten

They are two different processes.

 

1) Do I repeatedly shuffle around files that have "Overwrites and Overwritten" ?

That will only change which one is overwritten.

Other Managers call this is Install Order if it helps you understand, this is the left panes Priority column.

How Mod Organizer controls what mods win or lose conflicts when you drag and drop Mods about (other managers require uninstall all inbetween mods and reinstall to change the install order so it's not often done). Be aware that other sorting views exist but only this column order controls Mod Conflicts.

 

Someones told me that the Overwrites and Overwritten can be solved by changing the load order? Is this correct?

No never. Load Order is ESP ESM files loading into game, that priority is completely different and pretty much a standard system that must be followed.

 

Load Order use BOSS

Plugin Tabs Priority Column is Load Order starts at

0 for Skyrim.ESM

1 for Update.ESM

both are grey and unchangable

 

Other Tools

You must run BOSS and all other tools through Mod Organizer by setting the path to them in Gears Menu Icon otherwise they cant "see" Virtual Data Folder and only 32-bit versions can be run like this

Another tip the Great File Manager FreeCommanderXE will see "see" Virtual Data Folder when started using Mod Organizer

 

Java Programs work the same way for example

 

Clicking Gears Icon opens Modify Executables Window

I use for ENBManager and Changer which is a [·JAr] File

Title

ENB (Enhanced Natural Beauty) Manager and Changer [·JAr]; Tools for The Elder Scrolls

Binary

C:\Program Files (x86)\Java\JRE7\Bin\JavaW.Exe

Start in

{you can Leave this empty most times}

Arguments

D:\TES\Tools\ENB Manager and Changer\ENB Manager and Changer.JAr

 

That sets it up in the Drop Down List next to Run Button and for most tools Title and Binary are all thats required to set.

 

Think that covers last posters issues but for these advice posts to be useful they take a long time to make. Care and thought about accuracy must be considered as well as pesky updates that move the goalposts.

So please go to Support Forum it does not matter if it's STEP related. They are Mod Organizer's Support and on STEP for the better forums and advice only.

Even Fallout, Oblivion or New Vegas are supported there as Mod Organizer is for those games as well. STEP is purely for Skyrim.

The Main reason for the move was due to continued repeating of same few questions as soon as they got a page or two down and on Nexus that was every 10 posts.

This topic already 30 pages but Nexus is 600+. Even the most patient and helpful were sick to death of repeating same answers after about 500 times.

So use the Support Forums and most questions including every one I've answered here are already answered.

[AwfulArchdemon]

@Terriblypleased: your 'overwrite' folder is telling you that you have something 'manually installed'. You have something in your Skyrim\data folder. It's most likely a FNIS generation, and a SKSE\plugins\StorageUtil.save file.

 

Right-click the 'overewrite' folder, and choose 'create mod...'. You can then turn stuff from 'overwrite' into a mod, and install it as usual.

 

 

Load order has no effect on 'overwrite'. To change the order on the left, you can just click the number of the mod twice (not double-click though), and type the number in yourself (like I do).

 

 

Changing the one's on the right (esp's and esm's), just drag them where you want them. Your main concern is getting the mods themselves (left) in the right order, then the esp's/esm's, which is where TES5Edit comes in handy, if the game crashes at startup.

 

And about the 'game data' issue, that question is answered right on the OP. 1st page.

 

 

 

 

By the way, I've updated the OP. It's slightly more useful now, with posted youtube vids and links to other MO-related sites.

[gvman3670]

Terriblypleased PMed me this, and I think that if it was here he'd get more or better help than I can give. I haven't personally seen what he's seeing in his MO.

 

=====================================================================================================

 

Tried posting a pic of what my MO is looking like but it's only asking me for files from "My media" and I'm not seeing anything on my user account where I can add them so I attached it to this.

 

 

 

Apachii along with fnis and ethereal elven overhaul + about a dozen others are greyed out in MO with red boxes with with crosses in the centre as icons in the "flaged" section.

 

 

 

Hovering over flag it says "No valid game data" and when the check box is checked the mod does not appear on the right side with the plugins.

 

Apachiihair.JPG

 

Not a huge problem I loaded them with NMM and they worked fine with a few base mods. After loading everything though it crashes after the bethesda intro logo as it gets to the main menu.

[AwfulArchdemon]

Sounds like he installed them without making sure the file paths were in the right order. If the first thing you see when you unzip the mod is a 'data' folder, you need to rename the data folder to the name of the mod, and zip it back up with WinZip or WinRar (or 7Zip), then install to MO. You should have been getting a 'no game data on top level' error at first, though I've seen MO miss that once or twice.

 

You can also use MO to 'open in explorer' (right-click the mod) and drag the meshes, textures, esp's, etc out of the 'data' folder, and uncheck the data folder after you've emptied it (it's useless after you take everything out of it).

 

Hope I'm solving this thing for you Terriblypleased. If you need to post a pic, just use the [More Reply Options] tab at the bottom right of your window when posting. Then click [Choose Files] at the bottom left, and find your pic in whatever folder it's in. May I recommend Irfanview?

[Terriblypleased]

AwfulArch: I'm not sure what you mean by right clicking the 'overwrite' folder sorry.  I can double click the installed mod and I can find a folder tree inside the properties window that pops up but nothing like that so not sure how you got to the point you have posted in the first picture.

 

It kinda sounds like I should do another clean install? I installed fnis through NMM because it wouldn't work on MO and SKSE manually.

 

"Sounds like he installed them without making sure the file paths were in the right order. If the first thing you see when you unzip the mod is a 'data' folder, you need to rename the data folder to the name of the mod, and zip it back up with WinZip or WinRar (or 7Zip), then install to MO. You should have been getting a 'no game data on top level' error at first, though I've seen MO miss that once or twice."

 

I was under the impression that if you targeted a mod with MO it would unpack itself properly but I'm guessing that's not correct then?

 

Edit: By OP I'm guessing you mean the beginning of this thread? I'm in the process of removing skyrim NMM and MO completely and do a fresh install and follow the steps at the start of the page. See how it goes. 

 

[bob11]

Oh well, I suppose I'll contribute.

 

Overwritten and Overwrites tags:  On the left is your mod installation order.  It has priority numbers.  The higher that number, the higher priority a mod has.  So if mod A and mod B BOTH have a file in the same place named femalebody.nif, and Mod B has a higher priority number, Mod B overwrites Mod A's femalebody.nif.  Mod B is tagged as overwriting (you can open its tab and see exactly what it overwrites) and Mod A is tagged as being overwritten (again, check the mod's tab to see which files are being overwritten).  Mod Organizer will use Mod B's femalebody.nif when creating its virtual data folder, thus making it available in your game.  IF you want to use Mod A's version instead, all you have to do is move Mod A below Mod B, or assign it a higher priority number than mod B (or you know, move Mod B above Mod A, etc etc).  Then hit refresh (just in case).  You'll notice that the tags changed and if you check inside the Mod tags, you'll see that Mod A is now overwriting that file.

 

What good does that do?  Well, if you want to completely remove Mod B, you just untick it without messing around anything else, and refresh.  The game will then use Mod A only.  In all other cases without MO, you'd have to delete Mod B, then reinstall Mod A.

 

Plugin load order is on the right.  When people tell you to fix your load order, they mostly mean this one.

 

Also, if you don't know what you're doing, leave the Overwrite FOLDER alone.

 

About "no valid data":  Skyrim follows a folder naming pattern.  The main data folder is called Data, then it branches up to meshes, textures, etc etc.  Mods usually have to put files in folders that the game deems valid.  MO assumes that the Data folder is present in a mod and then checks for either an .esp file or commonly named folders like meshes, textures, etc, and notifies you if it can't see the pattern from the top level.  Fixing that depends on the mod.  The simple cases is when the Data folder is present below the top level and/or is named as something else, like Apachii.  Right-click the folder that should be the Data folder and click "Set Data directory".  If it's correct, it'll light all green.  Then there are the harder cases when the files are all over the place, but the rule is the same.  You have to either set or create a valid folder structure and put the relevant files in there.  You can either do that during installation or from Explorer after installation.

 

Hopefully you got all that, cause I'm not sure I could've put that simpler.

[eifrag]

"no game data on top level" means you are installing a MOD that is not nmm compatible or a MOD that is to be installed manually.

 

just click the manual install and drag all the MOD contents to <data>

then a message will pop "looks good"

[AwfulArchdemon]

AwfulArch: I'm not sure what you mean by right clicking the 'overwrite' folder sorry.  I can double click the installed mod and I can find a folder tree inside the properties window that pops up but nothing like that so not sure how you got to the point you have posted in the first picture.

 

It kinda sounds like I should do another clean install? I installed fnis through NMM because it wouldn't work on MO and SKSE manually.

 

"Sounds like he installed them without making sure the file paths were in the right order. If the first thing you see when you unzip the mod is a 'data' folder, you need to rename the data folder to the name of the mod, and zip it back up with WinZip or WinRar (or 7Zip), then install to MO. You should have been getting a 'no game data on top level' error at first, though I've seen MO miss that once or twice."

 

I was under the impression that if you targeted a mod with MO it would unpack itself properly but I'm guessing that's not correct then?

 

Edit: By OP I'm guessing you mean the beginning of this thread? I'm in the process of removing skyrim NMM and MO completely and do a fresh install and follow the steps at the start of the page. See how it goes. 

Not sure how to be more specific than "right-click overwrite". Highlight 'overwrite' with your cursor, and click the right mouse button (as opposed to the normal left-click we use to open files). There is no need to uninstall MO. Uninstalling NMM is what I did along time ago. MO will understand any mod that has the proper "file path". Uninstalling is futile as long as you have manually installed mods (mods unzipped into the Skyrim\data folder).

 

So, if you create a folder on your desktop for mod extraction purposes, 'unzip' your mod into that folder. If you see a 'data' folder inside, it is packaged for NMM. If you instead see meshes, textures, sound, esp files, esm files, etc, then it's packed for MO. NMM reads mods that are packed like this:

data\meshes.

MO reads files that are packed like this:

meshes.

The 'data' folder is what NMM looks for. MO looks for the files that would normally be placed inside of the 'data' folder.

 

Rename the 'data' folder inside the zip. Name it whatever the mod's name is, and zip it. Just install that into MO after you rename it and zip it.

 

If you need more help, please PM me. I don't want too many posts on this thread dealing with one problem.

[AwfulArchdemon]

"no game data on top level" means you are installing a MOD that is not nmm compatible or a MOD that is to be installed manually.

 

just click the manual install and drag all the MOD contents to <data>

then a message will pop "looks good"

I think you meant to say "no game data on top level" means you are installing a mod that is not MO compatible.

[RitualClarity]

 

Overwrite Folder

This one gives modders a lot of trouble so no surprise you are puzzled. Basically Overwite is a Temparary working folder and most of the time you don't see this used at all but any time you update mods it is used and emptied when that use is done it's the backup folder as when Mods are changed always copy and then move is used.

 

If Mod Organizer did not use 3rd Party software nothing would ever be left here. When it is it's because Mod Organizer has no way to know where to put the files or the program involved would create a new file or folder normally in Data folder, separate from normal Mods like TES5Edit Backups or Bashed Patch, FNIS also does this.

The main issue is because of the cleaverness of MO it puts all the new files created into the "overwrite" folder. Many programs used commonly through this comunity (perhaps others) created files during normal game play. FINIS is one example. NVSE Extender is another. Both of these constantly create files in the "overwrite" folder. This has to be monitored and can be a bit tedious. MO is a great step forward however this very example can lead into issues for those newer to modding or those not fully understanding the mechanics and how to handle MO.

 

Not to mention these "generated files" are persistant across "profiles" even when they really shouldn't be. Example different FINIS configurations some with beast content, others with different skelleton configs. NVSE extender is save specific, really shouldn't be "persistant".

 

The "Solution" is to open MO each time you leave or make changes. Especially important when combined with "profiles" as the "overwrite" folder is persistant (across profiles) and not profile dependent. That can really bone your game if you don't pay attention to it. Every time I have used MO it has generated files time and time again constantly due to the nature of the mods I have used. FNV, Skyrim both do this. I am constantly cleaning the Overwrite folder each time I decide to add mods or change profiles. On some occasions I have even screwed up my game by accident.

 

I don't know if this is even possible however might be a nice feature(S).

 

Default .

All mods have to be installed in to a "default install" folder. The "Default" is a base folder which all the "profiles" pull their mods from. Can't start a game from "default" should be prompted to create a "profile". Standard Saves from the game folder etc all accessible by this folder/ panel. Basically the place you go to create the "enviroment (s)" you wish to use in MO.

 

Profiles.

Must be created to start the game. Pulls the info from the "default" settings created by you. Make the needed changes to various settings priorities even load orders over the "default" settings. Here is where you put the customizatons you need for the current game. Import the needed saves from default or other "profiles" click start and play.

 

Overwrite folder.

Overwrite folders are "profile" dependent along with the "saves". With "profile" dependent Overwrite folders. Noobies and those not fully understanding MO mechanics or those that don't wish to micromanage their mod manager can just click and go. Any files that are generated in the "profile" overwrite folder would be generated by the actual mods used. Profiles changed means saves and overwrite folder changes with them. Only the "Default" would be the area that would be used to import and manage the massive mod collections you assemble.

 

The saves process and the overwrite folders processes are the confusing parts of what is a revolucionary mod manager. These two things create a larger learning curve for those just starting. Lock the saves, overwrite folder, and profiles together with a "default" or base where everything is installed to be used by MO and that should help streamline and make it easier for use.

 

I don't even know if it can be done much less if the creator would like this direction. Just some ideas. Yes I know i can post for feature request however I don't even know if these features are something the modding community even agrees with.

 

 

 

[Terriblypleased]

Ah well I was getting "no game data on top level" on things like Fnis and I was told it was compatible with MO ?

[lordofthedread]

Ah well I was getting "no game data on top level" on things like Fnis and I was told it was compatible with MO ?

 

You just have to move folders up to MO data folder, it's not hard and it is indeed compatible.

[RitualClarity]

Ah well I was getting "no game data on top level" on things like Fnis and I was told it was compatible with MO ?

 

Install manually. There is an option to change the folder used for the "Data" click and change and you will lose the "no game data on top level" issue. I actually check all the mods for this when I install even though only need to do so with those that don't work according to the instructions.

 

I come from when you had to actually make the archive invalidated file. Control freak.. Not needed so much with MO. Hard habit to break.

 

[AwfulArchdemon]

Ah well I was getting "no game data on top level" on things like Fnis and I was told it was compatible with MO ?

To install FNIS the way I do, unzip FNIS into a new folder. Take the 'tools' folder out, and put that in the Skyrim\data folder (manual). With the 'tools' folder in Skyrim\data, zip the rest of FNIS back up (without the 'tools' folder, as that's already installed now). Install that into MO as a mod.

 

Now you'll see 'tools' in the 'overwrite' folder. Click 'edit...' on the top right to add FNIS as an executable.

 

 

I don't use the default Skyrim installation path "Program Files (x86)". I installed Skyrim to my C:\Games path. My FNIS is located here:

 

C:\Games\Steam\SteamApps\common\Skyrim\Data\tools\GenerateFNIS_for_Users\GenerateFNISforUsers.exe

 

That is my 'binary'. Add your FNIS path to the 'binary' section in the 'edit...' tab on MO's menu.

 

Yours may be in the default path here:

 

C:\Program Files (x86)\Steam\SteamApps\common\Skyrim\data\tools\GenerateFNIS_for_Users\GenerateFNISforUsers.exe

 

Now run FNIS once (through MO).

 

Now, go down to the 'overwrite' tab on MO's main menu (all the way at the bottom on the left). Right-click it to pull up a small menu, and click 'create mod...'. This will put the 'tools' folder and all that FNIS generated into a mod, and you can then activate that mod in MO. No more 'overwrite' info.

 

If this is not specific enough, I'm afraid I won't be able to help further. I go back to school today until Thursday afternoon. I'll check back then to see how things are going for you.