Well, I have a Cayuga pair in my flock of chickens, but they don't stay in any of the coops with the chickens.
They DID when they were younger, but these two Cayugas, being all black, are my Ninja Stealth Ducks, on patrol around the property most of the night. They stopped going into the coop at least 9 months ago, because there's an auto door that closes and I think they figured that out. No wandering at night if they go in the coop.... They have various places they sleep, and I think they sleep a LOT during the day to make up for their night patrols.
When they DID stay in the coop, they had one corner where they slept together. Although I have feed in the coop, I also feed outside and water is only available outside of the coop. So the only extra messy place was their corner of the coop. No big deal - I use a deep litter method and scoop out gucky litter and add fresh over it.
Thelma and Louie fit in with their chicken flock members just fine.
For a while I had four call ducks, too, and they also had their own little place to sleep at night, not in the same coop with chickens.
Everybody ranges freely; they're not confined in a run.