Build points are set in a qvm. You can compile your own qvm, or declare the build points per map on the rotation using:
set g_humanbuildpoints [number]
set g_alienbuildpoints [number]
and putting that after every map in your maprotation.cfg.
The advantages to building it into your qvm, is that when a map is voted (off your rotation) the build points won't be set back to the default in your old qvm. So, if you just plop that line into your maprotation, and a new map is voted, you will not get your new build points on that map.
To set your rcon, add:
set rconPassword [password]
into your server.cfg
and use your rcon by typeing:
/rcon [password] [command]
into your tremulous console (in game).
Best Regards,
Kiwi
I was in a rush when I typed this, if you need further explanation or clarification, just ask and I'll post again when I have free time.