I love my covered sand runs. I top dress with new sand once a year.My husband made me a great scooper out of a Wal-Mart dustpan on a stick. He took out the bottom, and pop riveted 1/2 " hardware mesh in. I pick up runs once a day , and the sand runs through the mesh, but the poop stays in to be carted off.Combined with poop boards under the roosts, I can keep my coops pretty clean with no manure buildup, or flies.Deep litter seems to mean different things to different people. In theory, it is the piling of new shavings on old shaving, creating a new layer of bedding. It's great for waterfowl that don't scratch; thus, the top, new layer remains the top, new layer. I wouldn't do it for chickens. If your birds aren't overcrowded, four or five inches of shavings should last for a season or so, then out with old and in with the new.
I do use wheat straw in the sleeping coops so my chubby kids have somewhere soft to land coming off their low roosts. It stays nice and fresh for a long time due to the poop boards.
I think dry runs and roosts are key to keeping birds healthy. The other advantage to using sand for run bedding is that chicken manure does not seem to be to "hot" to use fresh on all my hydrangeas and other plants. I think it's the heat generated by decomposing shavings and manure that burns plants, not to mention that decomposing shavings actually deplete the nitrogen in the manure. Might as well get the benefits of the end product of all the feed the birds consume !