When I had two roosters who wanted to kill each other, now that was exhausting! To help cope with that situation, I built a wing coming off the main pen like an "L". It only has a tiny portion in common with the main run, and I have it blocked off with plywood so Flo can't pick fights through the fence. She can spend all day in the pen and even has access to a coop with a special nest box I built for her in one corner under a nice window. When I decided to let Penrod the rooster use the jail instead of his pen, it solved everything.
He's even happier now since he has a much better view of all the girls. There are several who have been plucking him of his lovely feathers so he only gets to be with them when I let them all out to free range. Except for Flo. She has to remain in isolation because she's a wicked little girl even when free-ranging.
At night, it requires letting Flo into the other side of this partitioned coop to sleep, and getting Penrod out of jail and put into his coop to roost. They each know where they are supposed to sleep, but it requires my being around to let them in. That's really the only hassle, if you want to call it that. If I'm not home in time, Penrod will get quite panic-stricken being trapped and not able to go in to roost. But there are ways around that problem if it comes up.