The ‘Material’ layer is used strictly to prevent the removal of stitches – first in the sense that the material stitches themselves are not removed, but additionally that the fabric inside the applique can obscure earlier stitches. As it is not good to have bulky stitches underneath an applique, those are removed. By way of example, you might want to overlap two or more appliques, and where they overlap, you want the minimum stitches necessary. Note that some designs do not have a separate material tack-down color. That’s okay to leave off in most cases.