I like the frixion pens which come off with heat, final press. It is also easier to mark before making the sandwich , ie without softness of batting/ wadding.
I've never had any trouble although I have read comments on here where they have left marks. I have three colours blue, red and black use on different colours try to keep blue with blue fabric etc., black used where colour match.
i also use them to mark my diary as you can rub out changed plans.