Yah, kinda confusing I suppose right off the bat. Lets see if I can get the jist of it.
1. Go download the latest 2.3 q3map2
2. Extract it to your q3 folder
3. Goto http://www.bobdev.com and download q3map2build (it's a GUI front end so you don't have to mess with all the crazy switches manually)
4. Install q3map2build
5. Configure q3map2build to point at the q3map2.exe file you extracted in step 2.
Play around with the GUI, and that should get you started. There are some switches in the light section of that GUI that you should check, but I can't remember them all off hand.
Shadow I'm sure has them all memorized. I'll take a look when I get home if he doesn't respond to this thread.