i sometimes just fmq my appliques down while quilting instead of stitching them first then quilting; i don't use invisible thread though (it's just me) i have never had any luck using invisible thread and have finally (after wasting lots of money and time) decided it's just not going to work in my machine so i match my colors or just quilt them down with what ever i'm quilting with. other than my invisible thread issues it has not been any problem stitching down the appliques this way, and i liked the way they looked on the back.
if you are unsure of the look try a small practice piece and see how you like doing it that way.