I use white chalk or soap on darks and a purple air vanishing pen on whites/lights. In both cases, I wait until just before I'm ready to quilt a section to mark it rather than marking the whole quilt at once. I've had the vanishing purple marks go away in as little as a couple of hours when it's particularly humid. The chalk will rub off and need to be re-done if you mark too far ahead. The soap stays put better than the chalk for anything that will not be quilted immediately, but I wouldn't expect to mark a quilt using any of these methods and then plan on leaving it unquilted for more than a couple of hours maybe a day at most.
Rob