I do completely clean out the coop and run area once a week. I spray the coop, nesting boxes, roost, floors walls, ceiling, doors and windows, then I put fresh bedding in the coop. I do let them out of the coop and run into the yard, if I can be outside to watch them, otherwise they roam off my property.
I used vetrx on my Rooster yesterday for scaly leg mites. There was also a bald spot on his wing which I treated with the Vetrx. I think that is from the mites as well.