I will quote myself from the server setup thread here
http://www.lucasforums.com/showthread.php?s=&threadid=111731&perpage=40&pagenumber=2)
I am running two busy Jedi Outcast servers and a Jedi Academy server, and I highly recommend Jedi Runner to anyone running a server from home or on a LAN. All three of my servers are hosted now, but I started out like many of you, a total novice running a small server on my home computer. Not only does Jedi Runner make it very easy to do complex things (custom map rotations, force\weapon disables, custom bot combinations, and much more), but the Help section is very good and explains a lot of the cvars and what they do. I also learned a lot by studying the configuration files that Jedi Runner produced. Very highly recommended.
You may have to tweak Jedi Runner to make it work with Academy, but probably not much since most of the cvars are the same. If you have Jedi Outcast, play around with it and study the config files it makes to understand how to configure your server. Jedi Runner is available here
http://www.gamerunners.com/modules.php?name=Downloads&d_op=viewdownload&cid=1)