Thank you for all the replies! I do have an enclosed coop, with a wood floor, raised up about a foot off the ground with cement blocks in the 4 corners. . I think part of the problem is that we put weed cloth under the sand to keep it from falling through the wood slats in the floor (There's very small gaps, but I was afraid it would all fall through). The chickens have begun digging it up and tearing it apart.
My plan today is to go out and empty the coop completely, including the weed cloth, and start over fresh with pine shavings, which I have 2 bales of from the local feed store. I also bought a mulching fork to help turn it. I already have DE, so I will start with about 4 inches of shavings mixed with DE. I have to figure out a way to hang their food bucket, too. We already have a hanging nipple waterer so that will be all set. I'm hoping it helps keep down the smell and general yuckiness of the coop.
I might spread out some of the remaining sand in the run. They have dug up all the grass and it's just a big mess of mud/dirt now.
Thanks again!