I'm guessing that you are running on a windows box. So, to startup a dedicated server without going throught the game use something like:
"C:\Program Files\LucasArts\Star Wars JK II Jedi Outcast\GameData\jk2mp.exe" +set dedicated 2 +exec server.cfg
for your shortcut. Then, you need a file called server.cfg in the GameData\base directory. What's in that file will vary widely depending on what type of server you want to run. I believe there are a few examples in the FAQ post above. It's not practical to have a config that shows "everything" because it's too cumbersome to manage. If you have specific questions about how to set something one way or another, just ask.