In that case, give this a try:
https://gbatemp.net/threads/installing-mods-hacks-for-citra-3ds-emulator.521228/
As far as I remember, Game Freak uses their own archives inside the RomFS, which also contain multiple files. So before you can use your modified files, you need to put them back into the same archive(s) they came from. Once the RomFS is unpacked, you can use GARCTool to unpack the .bin files, replace whatever you want, and repack the folder again using the same tool before the RomFS is ready to be repacked with your edits. PKSM by itself does not seem like it allows you to repack the archives. Well, it is a save editing tool, not a modding tool after all.
GARCTool:
https://projectpokemon.org/home/forums/topic/33035-kaphotics-xy-tools/
The tricky part is figuring out what file(s) the things you want to edit are in, since there are no filenames. There are probably incomplete lists scattered around the forum that should have most of the things people would want to edit.