ok for ctf, team spawn points are predetermined in the map, by
info_player_team1 or info_player_team2. These are included in the bsp. I'd suggest the point that u use for spawns prior to team choice be info_player_deathmatch or info_player_start (if its an id map).
If you only need 2 teams just download 3wave 4.2 and convert the id maps yourself, and use the teamspawns there?
edit: and yes this would require changing entity () SelectSpawnPoint