Dannii, is your duck sitting on the nest? I'm going to assume that you have a broody duck sitting on the eggs. Ducks are much more easily disturbed from their nest than chickens are so if you start to modify the house there is a risk that she will abandon the eggs. If you want her to keep sitting on them then I would not make any changes to the house yet. I would try to clean the nest though if it is poopy (has she pooped in it?) When she is off the nest to eat or drink can you use a small rake or something to gently move the nesting material to a spot where you can reach it? Then you could change the bedding.
It's also a good idea to fence off the area that your duck is sitting in so that no other ducks (male or female) have access to it. Use mesh that is half inch by half inch so ducklings can't get through it. Doesn't need to be a high fence, just a foot and a half will do. If other ducks can have access to ducklings they can injure or kill them.
When you have ducklings, take care stepping over the fence. Ducklings are fast and will run under your feet before you know it.
I hope that that is helpful. Sorry if I have misunderstood what you meant though
