I've done both ways. If I'm using a matching thread on black or near black, I'll often fmq with the back up, since that is usually a print fabric and I can see where I'm going easier. Try it both ways and do whatever works best for you. Try out some sample sandwiches and see. If you can make your sandwiches out of the same fabrics as your quilt, you'll be able to see what it'll look like on your quilt.