I agree with FrostRanger here. We put down pine bark (readily available here) and it did help with the smell, especially after a rain. Our runs are covered, but blowing rain can wet the whole run. Also, we throw scratch in their runs periodically, and pine bark hide some of their delicious...
We use pine bark chips which are easily available here. I add grass clippings in piles to the runs and the girls love to scratch the grass until it's well dispersed. Drainage is important, and cover over the runs is essential.