I will remove the freezer paper on some of the smaller pieces that are "tucked under" larger pieces, once they are secured. For larger pieces I will leave a small area, take a pin and run it just behind the fabric to losen the freezer paper and pull out the freezer paper. Then, I finish stitching my little opening.
I admit, sometimes, I have to cut thru the back of the fabric to get at those tiny little ones.
HTH,
Julie