If you have a smaller pen, or a tractor with a laying box or two, that is where I'd put my breeders.
In other words, I'd have my rooster and those 5 or 6 hens I want to use in the breeding program, in a separate pen or tractor. After 10 days, I'd start placing eggs from that breeding pen into the incubator. You can theoretically get 36-42 fertile eggs per week from 6 hens in the breeding pen.
That is likely enough to fill the incubator. Once you've incubated all the eggs you wish, you can release the birds, or "break up" the breeding pen, as they say.
This is one example of a breeding pen/tractor that we've used.

In other words, I'd have my rooster and those 5 or 6 hens I want to use in the breeding program, in a separate pen or tractor. After 10 days, I'd start placing eggs from that breeding pen into the incubator. You can theoretically get 36-42 fertile eggs per week from 6 hens in the breeding pen.
That is likely enough to fill the incubator. Once you've incubated all the eggs you wish, you can release the birds, or "break up" the breeding pen, as they say.
This is one example of a breeding pen/tractor that we've used.