I would think using a quilting bar would be the easiest, by far; no marking whatsoever.

I love my frixion pens; use them all the time - but it would take a lot of time to mark a complete quilt top! The only problem with the frixion pens I have found is if you use them on a dark color; when using the iron to remove them, there is a slight 'white-ish' line left behind. I would simply jump over any dark colors you may have, and eyeball it from the lines on the lighter colors.

(But I think I would try just using a quilting bar; no markings needed!!)