Vinnie,
As far as the height of the nest box goes, either 12" or 6" will work. The things to keep in mind.
Are you going to try a deep litter system? Make the nest box high enough to allow room for the litter on the floor of the coop.
The nest box MUST be lower than the perch. Otherwise the hens will roost in the nest box. They will then poop in the nest box.
As far as your multipurpose use, I would recommend a floor to ceiling partition because chickens kick up a lot of dust.
-RDG