Depending on the size of the pot, I put 3-6 inches of wood mulch on the bottom of them, separated by a layer of porous garden fabric. It allows for proper drainage, but it also stays moist without the added weight of rocks or stones. The roots do not sit in water, but it sort of seems to "self water" to some degree by keeping the lower layer of soil moist. This works best with annuals--because with perennials--the soil itself doesn't seem to last for more than a season or two and I have to empty it out and a add a new batch.
