I know how difficult this is! I use regualr chalkboard chalk, sharpened on a wide nail file...I know, not very accurate markings but, the general pattern gets there...I use an old, soft-bristled toothbrush, in the direction of the grain of my fabric...dampened in some water and tapped out (usually on the leg of my old blue jeans) to get the marks off.
I have done this with tailor's chalk (those odd looking, square pieces of stuff you buy for an enormous amount of money in the sewing store) and it worked well with the marking pencil (also very expensive, easily broken and down to the nub after just a few projects!).
Since most of my fabrics are things like silks and velvets, I assume the toothbrush method on cotton would not harm anything, since it hasn't done any damage to any of my stuff...YET! :roll: