I let everyone run together free-range, for most of the year. They have plenty of space and several houses to choose from.
When I want breeding pens, I pen the girls for three weeks, leaving the cockerels loose and free-range. Once the three weeks is up, I catch the appropriate cocks, put them in with their girls for a few hours once a week, and then turf them back out with their mates.
This has the advantage:
1. They get on with the job when they're in with the girls, instead of being penned all the time with them and getting bored
2. They maintain the cockerel pecking order, which minimises fights