I sew the appliqué on the front when it's sandwiched, as the pattern instructs. Time saver since you will not have to stitch quilt around the appliqué. (Unless you use trapunto method) But it's really a personal preference and your way would work, too. And, if appliqué has layers, I just glue baste (I don't do raw edge appliquing) them together as one unit then glue baste to quilt top. Then you just have to sew appliqués on whatever edge is visible. Saves time here too. I love this pattern but have never seen it finished so I'll look forward to seeing your project when completed.