Team 1 main flag: entry 64
Team 2 main flag: entry 65
Additional team 1 flags: spr_headquarters_flag_red*
Additional team 2 flags: spr_headquarters_flag_blue*
Neutral flags: spr_headquarters_flag_grey*
*Not sure I got the names entirely correct, and I might have messed up which one is team one and team two... erm, as long as you don't use the "code_only" things you should be fine.
Finally, place all entry points from 0-63 around the flags (so that all flags has at least one entry point next to them) including the main flags. People will automatically spawn on entry points close to their selected flag - entry_no doesn't matter as long as it's between 0 and 63.