The last quilt I did, I used the applique and quilted through all the layers and used it as an additional quilting. I think, as long as you know the back will look different, it can be really pretty.
I don't have any experience with hand stitching, but I assume that would work.
This is what the back of mine looked like after I appliqued a cross and 18 hearts onto the quilt.
https://www.quiltingboard.com/member...63-593870.html