I mark with a Dritz water soluble dressmaker pencil (white). I mark my top before layering so the marking is smooth. I agree that at this point, a paper pattern would be the way to go. You could really even use plain computer paper if that's all you have; I've done it before.
I know it's not what you want to hear, but the only way I've truly been able to deal with puckers on the back is to re-baste that section/those sections. It most often is caused by pulling the backing too taut when taping it to the floor/table. All you want to do is gently smooth it with flat hands & then tape straight down to the floor. You should not need to pull before taping. Also, it helps to tape the top & bottom first, then right & left sides (or R/L, then T/B), rather than trying to tape corners as the corners are the bias.
The other thing that can cause puckers is not starting your quilting with foundation lines. Foundation lines (typically that's SID -- but on modern or wholecloth quilts, you may need to draw lines to divide the space) help to stabilize the quilt so it doesn't shift during the quilting process. If you don't want those lines to show in your final quilting, you can stitch them with wash-away thread (YLI makes a great product).
I know it's more work, but I promise it really is worth it in the end as you save yourself from having to rip out a bunch of stitching that just set the puckers on your backing fabric.