Simply open the folder with the skin tone you want and copy the RomFS folder into: 

Citra/load/mods/0004000000164800 (for Pokemon Sun)

Citra/load/mods/0004000000175E00 (for Pokemon Moon)


If you are using RetroArch, then the citra folder is in RetroArch/saves/ (whenever your Pokemon games are) /Citra...