I agree with Dunster. The only exception would be if you were using a "regular" batting that required a maximum quilting distance that was smaller than the size of the squares you're making. But if you were using such a batting, it wouldn't be the same size as your top and bottom squares (because it wouldn't fray along with the other fabrics).
I apologize if I've only confused the issue. Just go with what Dunster wrote
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