This is somewhat a function of breed, age, and your coop set-up. If you do clip a wing (and you clip only one, not both) just fan the wing feathers out and with a sharp scissor, cut the tips of the feathers, about 1 1/2 inches or so, not into the quill part of the feathers, in a straight line. They can still fly a little, but can't get far and this throws off their balance and ability to launch. If you have large breeds, they seem to fly most when young and small and less as they get older and heavier. If you decide not to clip the wing, short of completely covering the run, you might consider attaching a length of poultry wire or hardware cloth (scraps) leaning in, along the top of your run so that if they fly up, they hit that and don't have anything to land on at the top. If you have small "flighty" breeds, you may have to clip the wings if you can't cover the run. Some chickens (banties, and smaller, lighter breeds) can fly really high. But I guess you've already discovered that!