WFA's Domination mode uses up to 3 "capture and hold" points. These capture and hold points are placed on the map using the dom_point entity (which you could find for yourself if you chose to look in the entities.def file)
*QUAKED dom_point (0 .5 .8) (-16 -16 -32) (16 16 16)
-------- KEYS --------
count: "Count (1-3)" : 1
-------- NOTES --------
count relates to the hud, 1 = alpha, 2 = beta, 3 = omega.
message : name of the location (text string). Above names are used if this is not set.*
You should place the 3 different domination points in different strategic locations throughout your map. During gameplay teams "capture" these locations and receive points for it over time based on how long they hold each point. As with all entities, you can use the gametype key to specify which of your entities (including doors, ammo spawns, player spawns, etc) appear in your map based on gametype, CTF for regular WFA games and COMMANDPOINT for Domination Mode.
I'm not a mapping guru, did I miss anything Rav or SS?