Agreed with JT and Nmin... If your run is predator proof and your climate does not present issues, I'd leave them to their devices. Minimum recommendation for space is 4 s.f. in coop and 10 s.f. in run per bird. Based on what I'm seeing, your coop/run may be a bit on the small side. They are sleeping in the run b/c they feel safer there. (higher roost, more room) Run and skirt are 1/2" hdw cloth, yes?