I use the fly paper. It works really well for both the chickens and the duck coops. Although the duck coop reguires a little bit more. Smelly little things they are. Lol! You dont even have to touch them just take them down and throw them away.
Go to your nearest farm store and by the fly traps that are have a yellow base and a clear globe thing over it. You add water and stuff that comes inside the unit in a packet...it smells sort of dead or rotten...and it draws in about a million flys and once in - they can't get out. Hang up a couple around your pen/farm and prepare to be amazed. They cost any where from $5.99 to $6.99 here in Nebraska.
Don't spill the packet contents on yourself - it stinks really bad but that's what makes it work as well as it does. Once it is hung up - your job is finished. Once it is full of flys you toss it and replace with another. These things really work! I hang our traps about 4 feet off the ground...a short one way trip for the flys.
It also helps to let your duck area dry out - move the water container to another part of the pen. You can also use "Stall Dry" or sweet barn lime in your pen and that will help too.