Is the batting cotton? I have found that washing quilts made with cotton batting gives them that nice wrinkled look AND hides a multitude of quilting sins.
I've used several different methods for marking designs, the most successful being marking the design on tissue paper, stitching through it, and then ripping the paper off when I was done. Chalk works okay, too, but tends to rub off too easily. For straight lines I use masking tape a lot.