For texture files, I know that you go into citra and go to Emulation on the top of the screen. Once you've clicked Emulation, go down to Configure. When a new window opens up, click Graphics. Once you're in Graphics, click on "Use custome textures" and "Dump textures". The textures will appear in a file called "dump". You find out where this file is located by right clicking your game on citra, and clicking an option that days something like "show where textures are dumped".
As you play the game, citra will grab texture files one at a time. This means that you have to play the game first in order to make texture edits.
When you edit the textures, give it the same name as the original texture, and put the new texture in a folder called "load". You do not have to delete or re-arrange any files in the "dump" folder.
I would suggest keeping every original texture that you're planning on editing in case you need to go back and start all over or you accidentally change the name of the new texture file incorrectly & can't find out what the original name was, because once a texture file is dumped citra will not go back and dump it again (afaik).
For anything else, I'm still figuring out.