Pencil can be a fickle tool. I have had it wash out beautifully but starched my top well so the pencil marks were really "floating" on the starch. I have heard of antique quilts that still have visible pencil markings. The graphite tends to imbed down into the cotton fibers and that is why it doesn't always wash out. I'm not sure there is anything you could use to get the marks out prior to quilting. The washing machine may be your saviour once it is quilted though.