If you want to put gravel in the run don't use the colored type, use a natural colored gravel, only because the colored type can get really ugly after awhile, and there is always the possibility of the coating coming off and the chickens eating it by mistake.
I am going to build a new run and coop this spring and plan on having the coop raised off the ground. However to insure proper drainage I will dig down at least 18 -24 inches, and line the hole first with 1/4" hardware clothe over which I will put a 6 inch layer of gravel, then some garden fabric ( to keep the dirt from clogging the gravel up, then a 6 inch layer of sand,covered by garden fabric and hardware cloth, then more gravel and sand. As the sides of the run will also have a 12" board running around the base of it inside the run area, I will be able to mix the top layer of sand, dirt, straw and gravel.