Food and water IN the Coop is very likely going to require Daily Clean out and bedding replacement in the coop. Ducks can be some messy critters. We put food and water in the Run.
The Run, being more spacious, can likely take more abuse before you need to clean it. Word of Caution...It is a good idea to remove the food at night. Leaving it can attract pests, or in our situation, a Bear tore through the fencing and stole the feeder. Fortunately no chickens were harmed, but Lesson Learned!...JJ
I currently have 10 chickens and I always have the feed and water in the coop. However, I have raised ducks in the past and know that they are really messy and get everything wet if given a chance. I had the duck feed and water outside but made sure nothing was left out overnight.