If it is a project that can be marked in small sections - I think I would use the chalky pencils. It does rub off - but if it stays on long enough to do the section one is working on - that would be good enough for me.
It would require marking the unquilted areas as one went - but that can be done.
I just don't have enough confidence in the pen types to use them. I had bought some "old" fabric that had light areas where it had been inked.
And as someone on here said - for heavens sake, do NOT NOT NOT use a ball-point pen.