That's what we have too. the coop above the run. They all cuddle together in a big box (two nesting boxes really, without the divider), but not in the nesting boxes that they lay in. I can see not wanting them to be laying in their poop though, so we are going to try and figure out a way to put...
Why does it matter? We don't even have roosting bars in our coop (its a little small), but they all sleep together and don't seem to care. Is it really a problem? We clean out their sleepy area every few days and never gave it another thought!