I would use the Frixion pen to mark it. Mark it prior to sandwiching it. It irons out when done quilting. Someone posted that the markings come back if the fabric is in freezing temps. That's not likely to happen with most quilts. I've had very good luck with the Frixion pens. What color is the backing? I think you'd want the backing thread (in your bobbin) all the same color. I'm leaning toward a light to medium gray color for the whole top.