I either embroidery quilt labels or use a pigma pen (used one for years on kids school items and it did not wash out)
I hate to mark on the top of quilts as I don't know what that mark may do in the years to come. So I use masking tape laid on the top and quilt along it's side. I never leave the tape on overnight and just use two strips at a time to line up the stitching, removing quickly after stitching. I don't like blue painter's tape as I can't get it to stay attached long enough to stitch. I know, some people will disagree with me about using masking tape, but after 40 years of using it quilting I have never seen the residue that people speak of. I believe the trick is to remove it immediately after stitching.