You need deeper bedding in the coop and the run. As in hay or straw, or other bedding piled about 8 inches deep. Most if not all of the dirt needs to be covered. Take your feed out at night, feed only enough for the day, or if you can schedule it, feed only enough in the morning, and then again in the late afternoon. Remove and wash out your feed bowls.
Put your water in a closed bucket, using nipples to water your chickens. Flys are attracted to moisture.
If a certain area gets poop and flies, throw scratch directly on it. The birds will scratch that area up, breaking up the poop, drying it out, and burying it underneath.
If these options don't help, you may have to look at the size of the area and the number of birds you have.
Mrs K