Right now my Pen setup is everyone is in the same enclosure, but I am not going to start hatching until maybe december/january.
Due to the fact that I have more breeds then I have breeding Pens I have made my own little plan making sure I only hatch purebreds. It goes like this:
Once all my pullets start laying I will seperate all roosters out of the current community enclosure.
Give the pullets 3 or so weeks to get rid of any eggs fertilized by whatever roo got the chance. Then whenever I want to hatch a certain breed of chicken I just put the pullets and rooster of the desired breed in a enclosure of their own for a day so he can do his thing and then put the girls back in the main flock and always put their eggs aside for hatching. That way I don't need a breeding pen for of the 13 + breeds and colour projects I want to have going.
Basically I have 3 enclosures = 1) Hens/community(winter), 2)Roosters, 3)honeymoon suit.
I just have to keep up on recognizing eggs from each breed, or I just get all my hens that lay the same colour egg bred by their matching mates and have a bit of a surprise when I hatch them and see which breeds eggs I have collected.
*edited to add* - I almost forgot to say only crossbreeds I have are the freeranging mutts I got that can do as they please. Nice to watch in the yard and not a big loss if the coyote or hawk takes one.
Anna