Your coop & run should not stink. We have no flies and no odor. We have 6 chickens and I spend maybe 10 min./day plus 2 big clean-outs a year to keep things clean and odor free.
We use pine shavings in our coop and 'deep litter' in our (covered) run. Ventilation in the coop is also important, a dry, open coop smells a lot less than a damp, stuffy coop.
In our coop we have a poop board under the roost which collects most of the dropping. The poop board is filled with StallDry (PDZ) which absorbs odor and moisture. I sift that out every day or 2 and throw it on the compost pile. That makes great garden fertilizer! The floor has about 6" of pine shavings which absorb anything else. Every few days I fluff the shavings with a rubber broom. We clean that out twice a year (spring & fall) and till it into the garden.
In our run, we have grass clippings, straw, hay, leaves, garden debris and pine needles. We add to it through out the year. It's probably 8 or 10" deep. Their dust bath is also in the run, filled with wood ash and peat moss, they fling it around so that gets mixed in as well. The poop falls to the earth underneath and decomposes. It usually stays dry since the run is covered but if the rain or snow blows in we fluff it with a stall fork. We throw scratch, fruit, veggies and other treats out there so the hens do a pretty good job of keeping it turned. We clean that out in the spring and till that wonderful composted soil into the garden and start over.
A lot also depends on the number of chickens & living area size. We have a large coop and run for my 6 which helps. We don't free range but that would help too.
We have 4 Black Sex Links & 2 Buff Orpingtons.
