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

Citra/load/mods/00040000001B5000 (for Pokemon Ultra Sun)

Citra/load/mods/00040000001B5100 (for Pokemon Ultra Moon)


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