I use a poop board under the roost with sand and PDZ(which absorbs ammonia) and sift it clean every few days, poop goes to compost.
Coop floor is vinyl and has kiln dried pine shavings a couple inches thick, totally change these out once a year(to compost).
Run is just dirt.
There is usually very little odor in the coop unless it is very humid, or someone has just dropped a fresh cecal poop, or I've been giving them too much fruit making for wetter poops, or it's very hot and they drink more water again making for wetter poops.
Run can get pretty stinky during snow melt season or heavy rain events. I just throw some dry organic matter out there and that helps dry things up.
Dry is the key to stink....keep things dry and they'll stink less.