I do raw edge applique with Wonder Under and either a straight stitch and inivisble thread or blanket stitch and a regular thread. If you're doing a straight stitch and invisible thread use a 60/8 needle and sew about 1/16th of an inch from the edge of your applique. An open toe foot makes a world of difference for machine applique!!
I'm about to start a huge raw edge project. It has 7 flowers, 66 leaves, a cardinal, and at least 10 snowflakes plus I'll couch down a vine for the leaves.