You'll likely have fewer issues using From2ch Lives with Better Cities as opposed to something like Open Cities Reborn, which not only "opens" nearly all the major cities into the Tamriel worldspace (so you never have to go into a loading screen when entering cities, just walk through the city gates straight from the outside) but drastically alters their layout as well (Anvil and Leyawiin in particular are practically brand new).
It's worth noting that I haven't encountered any major issues with the NPCs who travel between the OCR-modified cities, and they walk around just fine in the new city layouts too. NPCs that normally loaf around inside the inns/boarding houses also show up just fine. I'm not as certain about the NPCs that normally hang around the new merchant tents, since they don't show up in OCR.
I think From2ch Lives should play much nicer Open Cities Classic though. Classic uses the same concept of allowing you to walk directly into the cities through the gates from the worldspace without ever seeing the loading screen, but retains the vanilla city layouts. It's worth noting that OCC should play nicer with overhauls like WAC, but it's not as compatible with stuff like Oblivion Collector's Cards. Kind of a shame, since I really dig the Open Cities idea as you might've gathered by now.