One method I've seen is to use starch instead of glue stick. You can use spray starch, spray some in the can lid, and use a small paintbrush to paint the starch on the seam allowance. Then iron it dry. Now pull out the freezer paper and the starched edge is nice and crisp and ready to be appliqued to the background.
When I do this method, I usually make a double layer of freezer paper. (Just iron the two layers together.) The single layer is a bit too thin to hold up to the wetness of the starch. I think this is the method that Sharon Schamber uses.