I would put her in the barn if the dogs are going to get into the eggs. They don't mind males around normally. I don't know how long it takes for them to lay eggs, we have so many ducks we don't know whos eggs are whos. We incubate ours, but since you don't have a whole bunch of ducks, I would leave it up to the momma.

The duck may wander into a private spot where she won't get bothered, but she won't wander too far. What breed are the ducks? It's really hard to know, because your situation is very different then mine... good luck!