Whether you should spray or not depends on the active ingredients. I don't see why you'd spray for flies, though. Do you have a parasite (lice, mites, etc.) problem? If so, you might want to get some poultry dust (active ingredient, permethrin) and dust it around the bottom of your nesting boxes.
You can also get sprays with the same active ingredient. Many sprays use it. (Hartz Flea and Tick for dogs, for instance, though poultry sprays are cheaper).