I have 2 fly traps hanging in my chicken coup. They catch a lot of flies. I get them at Walmart.

http://www.amazon.com/RESCUE-FTD-DT12-Disposable-Fly-Trap/dp/B00004TBKM/ref=sr_1_2?ie=UTF8&s=home-garden&qid=1247488597&sr=8-2

I also sprayed a patch on the outside wall of their coup with Quickbayt. It is safe around poultry. I use the one that's dry in the bottle, you add water.

http://www.drugs.com/vet/quickbayt-spot-spray.html

http://www.valleyvet.com/ct_detail.html?pgguid=A580F0E9-E5C3-45EA-B6E1-F656F75F808D&item=39816&ccd=IFF003&utm_source=froogle&utm_medium=free&utm_content=39816

See the results in this post on my blog.
http://msredneck.blogspot.com/2009/06/only-good-fly.html
Ramona

Here is a link that might be useful: MY BLOG

There can be a problem if the chickens find where the flies are hatching and eat the maggots. They can develop a condition called Limberneck. Bot flies may also pose a threat to chicken health.

You probably need to clean and put down some shavings to absorb the moisture from the chicken droppings, especially under the roost.