Trisha, I'd put in the nestboxes just prior to them laying, maybe 16 or 17 weeks, so they could investigate them and be comfy with them, but you can put them in anytime you want.
At 12 weeks, they are still a bit young for your rooster to be with, but it sort of depends on his temperament. My rooster Hawkeye is around youngsters all the time and doesn't try to mate them, but my other young roo, Suede, would probably try to mate a six week old, the big pervert. Maybe it's because Hawkeye is older, but maybe it's his laid back personality, too. You want the girls to be large enough that if he does try something, they won't be hurt. I think maybe I would wait till they are at least another three weeks. You could try to let him out briefly and see what happens, but keep a close eye out on him.