Only clip one wing, of you clip both then they can still have level flight, an equal amount of force from each wing makes it possible to flutter up a little bit no matter how short you clip it. If one wing has more force than the other then it throws the bird off balance and makes it extremely difficult to fly. Also, go around the fence and make sure there is nothing leaning up against it or near it that the birds can hop on and then hop to the fence. How big is the run? You could probably cover it with netting if you want but you may need to put up some beams in the run to hold up the netting.