As long as your server uses V1.11, then you are safe from cheats.
Just search through the site for mods for your server, and read their readme files on how to get them to work (Crow King's Auto-Kick, DogMeat's Map Fixes, Soccerdevil & Bazooka Joe's Chat Filter, etc)
As for setting up your own server, here's two good guides to follow:
http://alliedassault.com/community/guides/bull/
and
http://alliedassault.com/community/guides/archangel/