There needs to be a tutorial on this.
In your configs/server.cfg file, scroll down to the bottom until you see this:
// ----------------------------------------------------------------------
// OPERATOR SETTINGS
// ----------------------------------------------------------------------
// Use "login password" at the console to obtain op status of said level
// Commands are restricted by level in commands.cfg
set oppass1 ""
set oppass1level 1
set oppass2 ""
set oppass2level 50
set oppass3 ""
set oppass3level 100
set oppass4 ""
set oppass4level 150
set oppass5 ""
set oppass5level 150
rcon_password ""
Change the oppass5 line to 'set oppass5 "mypass(Or whatever you want the password to be"'.
Now, just type 'login mypass' at the console and you have COMPLETE CONTROL!
Look other places for commands, but I'll give you a few basic ones...
newmap (mapname) - like map, but changes the server's map instead of the local one.
ctfmode (-1-4) - Changes the mode of play. I think they're...
-1 - Team DM
0 - DM
1 - Single Flag
2 - CTF <- default
3 - Siege
4 - KOTH