I tried both in an egg carton and just setting them on the bottom of the incubator. I prefer just setting them in the bottom of the incubator. Just personal preference I guess. You could just give it a shot and see which way you like better.Can I ask why you left them in the egg carton? I am going to be setting another round of eggs, WC polish and red shoulder yoko's, and am wondering if this might be an alternative after they come out of the turner...