I have been reading Harriett Hargraves book "Heirloom Machine Quilting" and here are some of her marking tips. (1) Use spray starch and press your quilt top before marking. This way, you are actually marking on the starch, and the marks will come out with the starch when you wash the quilt. This is especially important if you prewash your fabrics. (2) Use a HARD mechanical pencil when marking. Do not use a #2 soft pencil, as the graphite in the soft lead bonds with the fabric fibers. (3) Take a sample of the fabric, use the same batting and backing, mark the fabric and quilt it. Then wash it the same way with the same detergent that you would use on the quilt. (4) Don't use a dressmaker's marker, as they have wax in them. Dressmakers alway mark on the wrong side of the fabric and don't need to worry about the marks laundering out. (5) White chalk is good, but be sure to pre-test when using yellow, because yellow markers have sulfur in them, which can stain your quilt top.
Hope this helps.