Hi JustHatched.
How often are you planning to hatch? Your SIL's ducks, how many generations are they removed from the original purchased ducks? How big is her flock?
I am a proponent of pure-blood breeding, especially of the endangered breeds, which Cayugas are. Having said that, there is no reason to not to take all 3 animals (and in fact, would be the healthiest choice, as drakes are randy little birds who can damage a single hen from over-breeding). You will know that the blackish eggs come from the Cayuga duck and are pure bred; and the white eggs come from the Pekin, are not pure bred, so are best used for cooking.
If your SIL's flock is already pretty closely bred, you might consider looking around in the next year or so for another Cayuga hen to add to the flock.
If you plan to hatch frequently, and not add new bloodlines (recommended for bio-security), there is a type of flock/herd genetic management called spiral breeding.
http://www.pathfindersfarm.com/Spiral.html It's a bit complicated, and is more for the long-term breeder/hobbyist.
Good luck,
Tahai