You could have one rooster, hens of his breed, and then a variety of hens that lay other colors of eggs--that way, you could choose to hatch only purebred chicks, but without needing any separate pens.
Example:
Rhode Island Red rooster and hens.
Hens that lay white eggs (Leghorns, Hamburgs, Polish, etc.)
Hens that lay blue or green eggs (Easter Eggers, Olive Eggers, Cream Legbars, etc)
Hens that lay tiny eggs (bantams)
But no roosters except the Rhode Island Red.
Then: only hatch brown eggs. Presto, pure Rhode Island Red chicks!
All from a mixed flock in a single pen
(Roosters cannot be trusted to mate only with their own hens, so that's why all roosters must be the same breed to make it work.)
Edit to add: guineas will mate with guineas, chickens with chickens--so guineas are not a concern when raising purebred chickens.