The freezer paper on top method does not require you to iron down the freezer paper to get the applique edge. The paper is on top of the right side of the fabric. it is used as a guide to needle turn, then peeled off once the applique is complete.
Scroll down part way on this site to see a picture and a better explanation than I can give.
http://www.allaboutapplique.net/cate...back-applique/