you sure you got the latest version?
3-4 teams require some version of sep, you should have the latest version of sep installed, which is called SFE.
and to play a 3-4 team game, you simply need to load a 3 or 4 team map. there is no options to increase or lower the teams on any map. If the mapname starts with 4t_.... or 3t_... it's a 4 or 3 team map. however, if it's your server, you could maybe refremove a team or mess with the team balance thingies so you can leave one or 2 teams empty. Or maybe refmove ppl into 2 teams orso. Dunno what happens when you do that.
You could make 4 team versions of normal 2 team maps, but that usually results in very crappy unbalanced maps.
Anyway, i am not an expert, i am just bored atm, someone who knows it, will problably pop by soon and give some decent reliable info.