layout is not all trial and error - of course not. but it can often be very difficult to get it right even if you plan ahead. after some experience you'll be able to 'feel' what's right when it comes to many factors - but it really helps with early testing by REAL players.
a couple of things to think of can be found below. not all of these ideas apply to ctf-maps though:
Lunaran's Deathmatch Encyclopedialevel design patterns