Agricultural lime beneath the bedding will neutralize the ph and may help with odor and flies. Ditto on 3KillerBs suggestion of dry bedding and ventilation.
Does the duck house have a wooden floor or dirt floor?
What bedding are you currently using?
Do you keep water in the duck house?
How big is the duck house and how many ducks?
For mine......
My duck house is 5x7 roughly and houses 7 ducks.
I use pine shavings.
I keep the water in the run.
I have 5 big windows and additional vents.
My duck house has a wooden floor.
I can say when mine were babies in a brooder and played in water in the brooder it got really gross in just minutes. Getting that water away from the bedding made a world of difference.