How do I place the flags on a ctf map? can I control where those boxes with granades, health bulletproof vests and stuff will be created?
Is there a manual for mapmaking somewhere?

soldat-directory\MapMaker\Help\mapmaker.html

example would be:
c:\games\soldat105b\MapMaker\Help\mapmaker.html

there is everything you need for making maps and placing CTF flags :)