Question on Hatching Certain Breeds

Hi all! I've used Backyard Chickens website for much reading and info, but never posted. So here's a first for me! We've raised chickens for a couple of years and currently have near 100, however, all of our chicks have come from hatcheries across America. I've never actually hatched our own eggs. We have a couple of roosters (RIR and Barred Rock) and several varieties of hens.

I would like to hatch RIR chicks and maybe do a couple of our own hybrids, but I don't know how to do that with all free ranging chickens. How does someone control what Rooster mounts which hens and how do I know when the eggs are laid which are which?

I figured certainly people have raised from eggs strands of chickens and still allowed them to free-range. How would I do that and know what I'm raising?

Thanks in advance for all help!