I've done both methods. Since it typically takes me a while to hand quilt particularly a bed-sized quilt, I find that in many cases the markings rub off over time with all the moving and shifting of the quilt during the quilting process. So for the most part I now mark my designs as I go which means I am doing it after it is sandwiched. I use a #2 mechanical pencil for light fabrics and a white Bohin mechanical pencil for dark fabrics. Don't normally have issues with either of these tools washing out after completion.