I have not seen what you are doing, so of course you know more about it than I do. But if you are able to cut the two layers together then I would assume that both layers have exactly the same shape. I have made lots of pretty complex layered designs and if the two shapes have exactly the same shape then lining them up is not that hard. It does start to get more difficult when you have more than 10 or 20 small complex shapes that must lay in exactly the correct spot on the bottom layer. But that does not sound like what you are doing