It doesn't make a difference. My birds lay in the nest boxes because that's where they feel safe laying. I've put a variety of materials in there and they'll still lay in there. Currently I use hemp, which is on the coop floor under the roosts. They also drag in pieces of wood or feathers from the coop floor (I use wood chips in the rest of the coop) and it does not cause any confusion.I believe the idea is to help them differentiate between what they poop on and scratch around in, vs. what they lay in and don't disturb too much. (I've never tested the theory, since it seems way easier to just use a second material than to deal with wrecked, poopy nests.)