When I first tried using freezer paper, I used it on the wrong side and ironed the seam allowance around it. That didn't turn out real well and I didn't like it at all.
Now I'm using it on top and needle turning the seam allowance under. That is so much better. The freezer paper is only there as a guide for how far to turn under the seam allowance.
Another method I've tried, and the jury is still out on this method,is to sew the piece to be appliqued to tracing fabric. Slit the back of the tracing fabric so that you can turn it right side out. Iron the piece making sure that the tracing fabric does not show. Applique as usual.
In case you don't know -- Tracing fabric is found by the interfacing in Joann's and has a grid on it for tracing multi-sized clothing patterns. It's lightweight, never stiff, has no glue whatsoever (because it isn't an iron-on).