My advice would be pine shavings for the interior of the small coop. About 2 inches deep. If you have a droppings board / poop board, and it resides beneath the roost and they use the roost and drop on the board, that is where the majority of your problem will be inside the coop. Clean that often (maybe not daily, but often) and the 2 inches of shavings will last a month or so.
When the pine shavings looks like they need to be refreshed, drag them out into your run to mix with whatever else you have in there. My advice for the large outside run is about 6 inches or so of something that in a previous life was some kind of living plant material like wood chips, leaves, etc. My preference is coarse grass hay. Whatever this is should elevate the birds up off the dirt, which will help keep the odor and flies down, will not get muddy and keep the birds running around on high and dry plant material. This litter will rot down over time, so needs to be refreshed or replenished.......seldom replaced.