I have my ducks outside in a small coop with attached small run, during the day I open the door of the run and they free range (they dont go far from home) They swim in our small hand dug backyard pond (20 by 8 feet) and at night i throw some worms in the coop and they go to bed where they get locked in. They hardly eat any feed now that they wander during the day, they eat weeds and whatnot. I dont even have to water them since they have access to the pond all day. Honestly, they are effortless. Unfortunately trying to keep ANY animal confined to an unnatural area will naturally make for a messy situation. In a brooder they are a disaster but once they reach 3 weeks old and go outside they are great!
How are you using your run? Are you locking in coop at night and opening to run and then into yard or are they in the run some days?