They're *supposed* to spend their nights in there, it's vastly safer. If they huddle on the ground in the run, things can reach through wire mesh bigger than 1/2" square and pull out handfulls of live chicken meat; and even with hardwarecloth, having chickens sleeping outdoors in a tractor is just chumming for predators and ASKING them to test your tractor's security. Which is likely to be found wanting, if push comes to shove.
Anyhow, whereEVER they spend their nights will get all messy and pooey, that's just what chickens do.
I'd suggest making a way that you can easily clean out the floor of the tractor's house portion, and there ya go.
Good luck, have fun,
Pat