Steps to using mods in JK:
1. Create a folder inside your JK folder called "jkPatch".
2. Create a folder inside your jkPatch folder called "active".
3. Create a shortcut to your JK.exe.
4. Go to the shortcut's properties and edit the TARGET. Go to the end of the field (past the quotes) and add A SPACE and then add the following:
5. Put your patch in the jkPatch/active folder and launch JK with the shortcut.
You should really use this file structure because it'll be easier to manage which mods you have on/off this way. Also, if you ever get Patch Commander working, it uses this exact same file structure so you won't have to move your mods.