When working with two very large 4′ x 5′ freezer paper templates at once, it is probably best to come up with two different ways to mark them. That way, when you’re looking at the pile of pieces, you won’t have that sinking feeling when trying to figure out which number 21 goes where.
Next time I do something like this (although I usually don’t make two of the same project at the same time!) I’d probably use numbers for one template and letters for the other, or perhaps color code them, numbers in blue for one, black for another.
Hindsight. Oh well, happy quilting!