I read an article once, long ago, by a breeder of championship chickens who did this:
He kept the hens and roosters separate. When he wanted to breed a particular hen to a particular rooster He put them together in a separate breeding pen for a couple of weeks. He had nest boxes that the hens could go into to lay, and they couldn't get out until he let them, so he was able to know who laid which eggs. This seems a little extreme if you work a full time job and can't be watching your girls, but perhaps you could leave the hen with the rooster and just collect her eggs from there until you had what you wanted.
There was a more recent article in Backyard Poultry by Gail Damerow about making little wire baskets for eggs to keep them separate in the incubator to further track who is who.
Good luck with this project. It sounds very interesting!
We leave all of our roosters separate from our hens all the time.Only the hen or hens we want bred are put with the rooster we want in a pen together.I don't want all of our hens bred or just one bred over and over. Only the best of the breed or best egg layers are bred depending on which we are going for.