I would begin to sew down the fabric of the applique piece and leave a small opening...stuff a TINY bit of polyfil between the applique and the quilt top (enough to just give you the amount of pouf you want for the flower) and then finish your raw edge applique stitching. This way you would not have a cut in the back of your quilt. A friend of mine has done several quilts this way but she has always done it before the quilt is completed but I think this would work in your case too.
Pat