I have machine pieced, hand appliqued a quilt top (about twin size). The applique is in the main middle section and on 4 borders (middle with a small plain border on the inside and outside of it) and four inner corners. The main applique is a flower pot (free pattern from fatcatpatterns modified to make it bigger and easier --http://www.fatcatpatterns.com/images...owerPots_1.pdf to give you an idea of what I started with).
I plan to quilt it on a domestic machine and am thinking about just quilting around the applique but not through it. I think if I quilt through it, it will get too flat. I like that it is slightly puffy.
I have good ideas on how to quilt the non-applique part, but am wondering whether the back will look funny if the applique part is NOT quilted....If I do quilt inside the pieces, that means changing thread colors on top a lot.