Ducks aren't aware of breeds. The males will breed all the females, regardless of breed and in many cases species.
So you must separate if you want purebreds.
I have this issue every year with my geese.
The Roman Tufted females have a crush on an Embden male. My Pilgrim male loves the Embden girls. And my Roman Tufted male, as far as I can tell, hardly gets to mate anyone because he's so small. My 3 month old Embdens are bigger than him already and I do feel a little sorry for him.
Everytime I try to separate, though, they make such a loud comotion that I end up relenting and letting the flocks mix back together.