Holy crap. That's like showing us an image of the Mona Lisa and asking "How did Leonardo Da Vinci set up his easel?"
That particular bit was simply a moving mask applied to two images: one with the first model's head and another with a different head on.
Way cool and all. (And I do mean way cool!)
But you can't just walk in the the door and say show me how to paint like Picasso (as @Palocono has said).
Stop motion like that takes years of technique to develop. My advice is to shoot some stop motion on your own and play with it. Only by doing do we learn. There is no mind meld (software)... Poof! ... now you're an animator.
I wasn't actually saying that. I meant of all the questions that could have been asked about that amazing video, the one that was asked was about a very minor effect. But I guess you have to start somewhere.
It looks like you're new here. If you want to get involved, click one of these buttons!