place the mods contents each in their seperate folder in your GAMEDATA directory and makesure each of those folder has a description.txt with the mod's name in it. then go into jk2 mp, click setup, then select the mods menu. you should see a list of the mods in the window in that screen. select the mod you want to play and hit run.
some mods like promod, will include a bat file that shortcuts to that mod in gamedata directory so you do not need to go through the normal jk2mp window