I've made a few baby quilts where I fused then sandwiched and then raw edged the appliques. I used black thread to help them pop...and I LOVE the look on the back. I have appliqued before the sandwich and then just quilted around the appliques. But sometimes, to me, that leaves too big of a space with no quilting at all. And I don't really want to quilt over the applique in that instance.
So it depends -- partially on what I want the back to look like too.....and how much quilting on want on the actuall appliqued part.