Ok, you have to place the .dlls in their own folder in the /gamedata and then run the jk2mp.exe with the following arguements:
+set fs_cdpath "yourgamedir\GameData" - Makes the game treat this directory as the root directory. It will look for everything starting in this directory.
+set fs_game "yourfolder" - sets the game folder to load stuff out of in addition to everything in the /base folder
+set vm_game 0 +set vm_cgame 0 +set vm_ui 0 - Sets all of the game components to run in .dll mode if they can. After you get into the game, you can check to see if the .dlls loaded by checking the related cvars. 1 should mean to it loaded correctly.
Please note that I could never get the client side (cgame) to ever run in .dll mode. I beleive it is a bug in the game.
Your command line should look something like this:
jk2mp.exe +set fs_cdpath "D:\Games\Star Wars JK II Jedi Outcast\GameData" +set fs_game "MotF_Test" +set vm_game 0 +set vm_cgame 0 +map FFA_bespin
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