My chickens don't bother with flies except to snap at the dumb ones that get really close. I used to have a problem with flies. Now I treat my run with stall dry after it rains and use wood chips in the wettest parts. When the wood chips start to get icky (time period depends on how much rain) I rake them out, apply stall dry (heavily in the icky areas), and top off with some woodchips. I don't use the chips very heavily, just a light sprinkling except in the areas that get the wettest.
My chickens free range during most of the day and only spend the night and morning locked in the coop/run. I don't let them out until about noon because I work nights.