You may already know this but I'll go through it anyway, it may help you plan.
It takes about 25 hours for an egg to go through a hen's internal egg making factory. It can only be fertilized in the first few minutes of that journey. That means if a mating takes place on a Monday, Monday's egg is not fertile from that mating. Tuesday's egg might or might not be, depending in timing. I would not count on it. Wednesday's egg will be.
A rooster does not necessarily mate with every hen in his flock every day, but he doesn't have to. In the last part of the mating act the rooster hops off, his part is done. The hen stands up, fluffs up, and shakes. That fluffy shake gets the sperm into a container near where the egg starts it's journey. That sperm can remain viable in that container for 9 days to over three weeks. That means he only needs to mate with her once a week to keep her laying fertile eggs. It also means you need to keep a hen isolated from any rooster you don't want to be the father for a month before you collect an egg to hatch.
To me this gives you three basic options. There can be variations of these. You can build facilities and keep every flock separated. Might be expensive and could be a fair amount of work.
You can try housing them all together when it's not breeding season and separate them as necessary to get genetically clean eggs. Sometimes this works, they get along great. Many people do it this way. But sometimes it doesn't work, the boys just can't get along. There is only one way to find out.
You can house all the girls together and all the boys together but in a separate location. Usually if there are no girls to fight over the boys don't fight much. Usually. This way the girls are always genetically clean so you can isolate them with a rooster and get hatchable eggs in a few days. You still need breeding pens.
You'll need different facilities for each of these methods. Managing them will be different. I'd suggest trying a method that would be convenient for you and see how it goes.