I'm still relatively new to this too, but I've read a lot, so here is what I know:
It depends on how the site drains. For example, my run is on the highest point of my yard with very sandy soil. I shouldn't have any drainage issues. However, if I did I would put pressure treated 1x4's or 2x4's around the bottom. Then I would make four 4'x4' (or however many you can fit) frames made of landscape timbers covered with some sort of netting (something the chickens could walk on) and space them around the yard with some sort of ideally perennial high protein greens planted under them (chicken salad bars). After these were laid and planted I would put pea gravel around them (this is what the boards were for- to keep the pea gravel from spilling around the yard.
That's what I would do. I plan on doing the salad bar part, and just hope I don't need the pea gravel. I may eventually mulch around the salad bars, once they've killed all the grass.