If I were you, I'd have a go with a practice sandwich to see if it will work. I've never followed a drawn pattern, but I imagine it would be easier than trying to draw without a stencil (which I am terrible at!)
I took a workshop recently and the tutor recommended using watercolour pencils to mark patterns with. I haven't tried it yet, but it makes sense, and she said she'd tried all the different "quilting" markers and these were much better! Also frixion pens might work, as the marks disappear when ironed, but can be brought back with a little while in the freezer, they then apparently wash out completely, although I have not tested this either!
Good luck :-)