I use the deep litter method. I rake under the roost a couple of times a week, just a minute or two. I also sprinkle liberally with DE and Sweet PDZ, which is to keep horse stalls dry. There is another product called Stall Dry, but I like the Sweet PDZ better. I get it at Tractor Supply. It absorbs water and smells. I sprinkle it on top of the litter, then sprinkle DE. If needed I will add more litter and then give it a good raking to give it a good turning. I do this about once a month, more if we have a lot of rain. I change the litter only about once a year and do the good turning by thorough raking once a month. My birds all seem to be happy and healthy and I have no problems with flies. I have poop boards over my nest boxes and try scrape them every day, but sometimes they go every other day. I sprinkle DE over the poop boards after I've scraped them, too, and in the bottom of the nest boxes when I change the hay.
