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Not necessarily. I have my nesting boxes with a poopshelf on top of them and then the roosts. I don't have chickens yet, my peeps are due to arrive on 9/22, but I don't see why this setup wouldn't work. The location under the poopshelf gives them a dark place and privacy where they can do their thing.
I wouldn't place any nests under your roosts if you can avoid it, poop board or not. At any given time you may have to evict a bird from sleeping in those nest boxes at night and walking, or bending over under, a roost full of pooping birds is like asking for poo hair. Also, any birds that are low man...er...woman.. on the totem pole may just find that it's much easier to just sleep in the nests than to fight for a spot on the roosts.
This, again, leads to poop in your nests.
Best possible solution? Nests on one end of the coop, roosts on the other, nest boxes lower in height than the roosts. Nest boxes nearest the door and nearest the feeder.....so you can collect eggs and feed without tracking through the greatest concentration of poop. Also, if you have a broody, she can get down and eat/drink without spending too much time off the eggs and another hen hopping on to lay a fresh one in her clutch. Also good to have your feed can right next to the feeder and away from the roosts so the birds won't roost on your feed can and leave their poopy treasures right where you lift the lid off.