I just marked some flannel cutting lines, and they were all wavy and not straight at all, so it is a challenge. However, if you aren't stitching straight lines, I would use a colored chalk or soapstone. You can get some high quality chalk (that will wash out) in mechanical pencil style, which means it is very thin and will make a great marking line.
Happy Quilting!
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Penny Halgren
TheQuiltingCoach