What does everyone here do?
I have a large nesting box that is broken down into 3 tiers. The bottom tier has 2 boxes that are 24 inches across. The middle section has 3 boxes, about 16 inches across. The uppermost is 4 boxes of 12. Each bird has a box they prefer. We also keep golf balls and old wooden eggs in the boxes to encourage. I have a few that lay under the boxes, but not many. I also have 2 covered cat litter boxes that some prefer to lay in, they're on the floor. I use pine shavings in every nest and then all but a few have hay over top of the shavings. The girls love that.
The rest of the coop just has pine shavings (and poop/feathers). The outside of the run is dirt/leaves/etc. In winter when I need to do a coop clean I'll just toss the shavings out onto the snow. It makes the birds want to go out more, and it soaks up some of the mud in spring when things thaw. I've been doing that for years and the run still looks dirt, so you can't really tell. I do have a larger size run than most people do, though.