i just reinstalled JK:JA again and i felt that i should download a few mods and skins to enhance the gameplay a wee bit but... ive copied all those pk3 files to every folder in the ja folder and nothing shows up in the mod menu.
For maps & skins, just drop them into your base folder and they'll kick in automatically when you choose your map/character.
For actual gameplay mods, I believe you create a folder for each one in your GameData folder and drop the pk3's in their appropriate folders, then you can turn them on/off in-game. I say I believe because I don't use any gameplay mods, so don't hold me to that one ;)
B.
Remember to read the readmes for the given mods. Some mods, like mine (OJP), automatically install to the correct directories if unzipped to your JKA directory.