I use pine shavings in the nest boxes. The sand in the run is turned over by the chickens in the course of their normal activity, so cleaning is not needed. The poop gets turned under and recycled by composting.
The layer of sand in my run is deep enough that water does not stand in the run.
I am on the Oregon Coast where it is wet a lot! My run meaures about 27' x 12'. I put down a couple inches of gravel and several inches of sand. I live downtown so I am doing my best to avoid smell, flies, etc. I have 10 large hens. Do you think I will have problems when it heats up outdoors if I don't clean the sand? Thanks for your help! I really appreciate it.