So they will be covered in poo every morning? Oh no!
I will have to close the upper compartment of the hutch every night so they dont sleep in the nesting boxes. how thick should the roost be? I heard a 2 by 4 is good because it shouldnt be too thin or round so its easy to be on.Is that true? Also do roosters need a nesting box too?
Close the nesting boxes until the hens get old enough to lay. You want to encourage them to use the nesting box for just laying eggs.
Boys (cockerals if the are under a year old, or rooster if they are over a year old) do mot need nesting boxes at all. The nesting box is only for pulleys and hens to lay their eggs, and nothing else.
Yes a 2 x 4 with the 4" side up is am excellent roost. It keeps their feet comfortably flat on the roost. In freezing weather, it is essential that their feet are flat on the roost, so their chest feathers cover their feet and keep them warm. If they are always in the house, this isn't a concern, but it's still better to have the 4"side of the roost up for them to perch on.