I had a half bale of Bermuda hay my horse refused, so I was using that as bedding in the nest boxes for my 2 month old BSL and x2 3 month Aus... they liked to poop in that at night, because they were also eating it, so the nesting boxes got cleaned every day and new hay put in.
Now they are on straw from a compressed bale, which is 6 - 8 inch pieces, not full length straw stalks.
I do not think they like it as much, because there is now more poop under the two roosting perches on the tray than in the nesting boxes. 
I take the tray out and hose it off every day, and wipe the roosting perches down at the same time, I just use water and lemon/vinegar dish soap on the cloth...
Now, just grabbing a handfull of straw from the nesting boxes that has the poop and replacing that, instead of the entire nesting material.
The coop itself is on wheels, and I move it every few days around the 1acre paddock (it's mainly dirt and weeds, I am in N. AZ), so the poop in the run is not an issue.
Their food and water containers get cleaned every day, as the dust gets into everything.