Slowly reading all the comments on this thread but I have a question. I am in the Pacific Northwest. I am going to put the coop in a place where the rain water doesn't settle and I like the deep litter method sounds like you dont scoop poop you just keep it dry and keep adding items such as straw, dry leaving, pine shavings and household items like old bread, egg shells etc right? Do you do this in your run only and still clean out the coop and nest boxes? What should I do on the floor in the run if I am worried about the soil getting too wet through our lovely rain storms. I am not sure my run would stay dry during our rainy season. Suggestions?
You could put down a six inch layer of rock or gravel and then add you deep litter over the top of that. That way you would have good drainage underneath the deep litter. That is the method we use for our horse stalls to keep the urine from pooling in the stalls and it also keeps the ground water out of the stalls when we have heavy rains. It wouldn't hurt the birds even if they dug through the deep litter down to it.
I use deep litter in the coop also and only clean it out once or twice a year depending on how deep it is. When I need to clean out the nest boxes I just dump them in the deep litter of the coop. I usually don't have to clean them as the birds seem pretty intent on kicking the nesting materials out of the nests on a fairly regular basis.