For flies, a few ideas.
The Little Tree car air fresheners, Vanilla flavor are said to repel flies. Not too close to the duckies, when you first open the freshener the aroma is very strong. I put one or two near the door to the night pen.
Fly traps - you can make your own from two-liter soda bottles, duck tape and duck poop, or buy one. Some are just a few bucks.
Fly predators - a slightly slower long term solution, but they help keep the flies from getting ahead of you, and eventually may start reproducing a population so that they keep the fly population down.
Cover/compost the poop - once it is cleaned out of the brooder area, mix it in with sawdust or soil, and cover it with leaves or mulch.
Diatomaceous earth in the poopy mulch ought to help reduce fly larvae - I believe it kills soft-bodied insects.
