You will need to separate the breeding pairs into individual pens and wait a while before incubating anything to ensure the right male has fertilized your eggs. Set up a bachelor pen out of line of sight from the hens and breeding pairs to stow any non-breeding cockerels. Look into line breeding - it's more for large-scale production, but has some good pointers on managing your line. With 5 breeding pairs (hopefully not all related), you can get started on this method for breeding the traits you want in your custom cross.
I wish I had the space and zoning to play around with this sort of thing. Must say, I'm jealous.
