Hope you have a gentleman for a rooster. You might benefit from reading any of
@Shadrach 's articles, he is very knowledgeable on hen/rooster/flock dynamics. Hens invite a roosters attentions and a good rooster respects the hens.
Being a hen locked up with nowhere to run, trapped with a potentially rough, and relentless rooster in 5 and 10 square feet, a rooster who has no manners or training by an experienced older rooster, sounds like a nightmare for the poor hens. Be careful who you put in there together.
Sorry but unless I am mistaken or off-base this sounds like a plan you have to raise and sell chickens in an ongoing breeding program, correct? Can you put the hens and a rooster that you want to breed into a large proper run and coop of their own? Long term, that is a more healthy and humane way of going about it and the way I've seen breeders do it here on BYC.
You might concentrate on a certain breed for your entire flock and sidestep the whole separation issue. Also look at
@RebeccaBoyd 's posts here or ask her advice, she breeds chickens and sells chicks in a free-range situation.