Pretty quilt. Can you be more specific as to which fabric you are having a problem with? Is it your sashing or is it the fans? I am thinking your solid background will be fairly easy to see marks on.
Depending on how complex your stencil is you could try using freezer paper to make a template to quilt next to. This would only work for a fairly simple design like clamshell or egg and dart, heart shape or leaf shape. You can make a template out of your freezer paper, iron it on to your quilt, hand stitch next to it then peel it up and iron it down again. You could also do this with shelf liner paper that is sticky on one side, but don't leave it on the quilt for any length of time (like more than a day) as I would not trust the adhesive to not come up all the way if left on for any length of time. I am assuming you are not hand quilting in a frame with this suggestion as well.