I have not used liquid based marking tools because of their long term effects on your quilt top. The information I've read says that the chemicals in these pens can break down or weaken the fibers in your top, especially if left in over time. Another thing I read was that heat and laundry soap can set the marks. The recommendations for using this type of marking utensil is to mark your top, quilt it right away and then immerse the quilt in cool water until all the marks have disappeared.
Since my quilts get quilted over a period of time--sometimes long--I don't take the risk. But I also know people who mark their top, quilt it in a week and then soak it like you're supposed to and they've never had any problem. I just can't quilt anything that fast.