In my research it seems that as far as rock placement goes, the best idea is to build up reeflike areas and leave some areas of open swimming space... obviously there are no 'written in stone' rules with this sort of thing, go with what looks good to you. If you are keeping large, fast swimming fish, open space will obviously become more important.
So, you have some stuff building up behind rocks? It almost sounds like you don't have enough flow... while flow pattern is important too, are your rocks piled against the back of the tank? Do you run a sump? Any external pumps of any kind? I doubt having any amount of detritus collecting anywhere in a marine tank is a good thing...
Mind you this is coming from someone who hasn't even got all the equipment for his tank yet
let alone had water in it for 6 weeks.