to make a capture the flag map, or infiltration map, all you have to do is save it as ctf_the name of your map, or inf_the name of your map. oh, and by the way you also have to put the flags on the map. good luck with your map making!
Yeah, but the map maker tutorial is very light and vague. The best way to learn waypoints is to read the tutorials written by the best mapmakers out there. I recommend this one by bb_vb.
Of course, this is useless on it's own. Open one of the official maps which come with the game and look at the waypointing, and how it works.