Penny...Your blocks are lovely! Only you can make the right decision for you, but when I do applique, I do the blanket stitch or whatever I am going to do to actually hold the applique in place on each individual block...prior to sandwiching the quilt.
Then when I sandwich, I do an outline stitch right outside the outer edge of the blanket stitched applique...then continue and do whatever type of quilting I want.
Good luck...this is going to be really pretty!