You just need to follow folder structure.
Illusion games are usually modded in /abdata, and plugins must follow the right folder for different games (Honey Select use plugins folder and Koikatsu Bepinex, for example).
You download a mod, extract it, see folder structure and copy-paste exactly like they should be.
Abdata in abdata, chara in chara and so on.
If the game in question is KK, you can use the link above.
If Honey Select or Playhome, it is really copy-paste in the right folder. Of course you'll want to use necessary mods, like IPA (and patch the exe).
When asking for help, try to be a bit more specific with your problem, like which game, what you did to install them, how you tested, how they should work and are not, and etc. It makes it easier for others to try to help.