I've used red to mark pink fabric with no problem. I was also hand-quilting with red thread, so if it did leave traces of color, I probably would not have noticed. I have also used blue, green, yellow, orange, purple without problems. I do try to somewhat match the color the the fabric so that any traces left will be less noticeable.
Julia > From what I have learned from other machine quilting groups, not all Crayola