I put a thin layer of Pea Gravel in my run. My run is about 15x14 for 7 birds and is not covered. I added the gravel after I had read on BYC that it is not good for chickens to be in a muddy area and we had a really wet spring. I let my chickens out of the run when I am home to watch them so they are able to get some grass, seeds, bugs and such. I have not noticed any problems and the chickens are able to scratch through the rocks and get to dirt.