I'm having the same problem here Clayglen. We're in South Louisiana and the recent rain combined with the 90+ temperatures have turned our coop and run into fly heaven! It's disgusting. We use sand in the coop and run but it's been so damp lately that it hasn't really been doing it's job.
I've read everything from vanilla car air fresheners around the coop, water traps, fly paper and bug zappers. I've also read that certain types of herbs (basil, lavender, mint and rosemary) are natural fly deterrents. Muscovy ducks are also supposed to be great at keeping flies down as they'll eat insects happily. Our neighbor has a bunch and we're seriously considering getting a couple since they also really enjoy the constant damp weather.
If it's dry where you are, diatomaceous earth is great for getting rid of maggots, it dries them out and kills them and won't hurt your chickens, even if they eat it.
And finally, good housekeeping really is the best way to get rid of them. Just remember that for every miserable pile of poop you rake up, you're guaranteeing a fly-free future for your barn or backyard, lol!
We're probably going to employ a bunch of these techniques today as we set up their new run and clean out the old one so I'll let you know which, if any, work best.