Hi,
I can't speak to waterfowl yet with regard to fertility as I've been so swamped with my chickens that I just ain't gonna get around to breeding my ducks or Pilgrims this year.
However, I thought since nobody mentioned this, I'd mention it. With chickens, I put the cocks over the hens and make sure I see them mate at least 2x. Then I wait two days, crack the egg open and check it for fertility. If you're not familiar with that, there is a great thread on here that shows pics on how to make the determination.
There is some debate on the length of storage but hens will store a rooster's seed for (most say) up to two weeks. Some say longer, some say shorter. So I take my roosters out and then put them back in after a week. So far, I've had no fertility problems doing this.
A search on here or Google would probably tell you in short order if the same holds true for waterfowl.
Hope that helps.
God Bless,