My run is separated into 2 areas which I can close off with a door in between. The one run is tarped and the ground is covered with about 2 to 3 inches of small river pea rock, which the girls love. There's never a smell. I keep feed and water in this one. The uncovered run is simply dirt, which I turn with a spade periodically, it never has a smell either, probably because the girls scratch, dig, dust, and sun in this one and it does get rained on.
I use premium fine pine shavings in the coop itself, which I dust lightly with a food grade diatomaceous earth; floor, roost, and nest, and this is stirred into the shavings, lightly dusted down on the roost, etc. The coop gets cleaned completely out periodically and the residue piled up for later use as amendments to the lawn/garden (It doesn't smell either and makes great fertilizer).
My girls are healthy, happy, lay an abundance of eggs, and don't have any problems with mites or other crawlies.