The darker the line, the easier it will be to see through to your other papers. I usually just stick with a normal pencil until the final stages. If your paper is quite a bit thicker (so if it's illustration board or watercolor paper) then it will be hard to see through, and for something really thick, I would do a different method to transfer the final image.
But if you mean like it's hard to tell the difference between your lines--then yeah I can get that. You sort of get used to it after a while, turning on and off the lightbox to get a sense of what your top image looks like.