A label can be embroidered on the back piece only, that way, when you put the quilt together, the stitching on the back of the embroidery design doesn't show.
You could also have labels embroidered and attach them to the back of the quilt with hand stitching after the quilt is done. Karenchi, Sewbusy, gail-r (she actually is in the business of making quilt labels) all belong to this board and do labels, as I'm sure there are others.
You might try PM'g them.