My preferred combination for stitching is a black & white chart and a colored pencil. I never use marker or highlighter as I would be paranoid about somehow accidentally dropping it on, or brushing against, my fabric. I have heard horror stories, and I'm sure you have as well. For me, a quick sweep of the colored pencil on the section I've just stitched is sufficient to keep my place.
I avoid color charts, if possible. A color chart won't prevent me from stitching something I really like, but if I have the option, I always choose black & white. For most color charts I've stitched, I find that a silver metallic pencil will do the job. The metallic reflection provides just enough contrast to the color symbols to see where I've marked. I use the silver metallic pencils found in the sewing notion section of craft stores.
However. I occasionally run across color charts where the chosen colors, together with the color saturation, just absorb the silver pencil (which are not heavily pigmented in the first place) and it's difficult to see the marked sections. Solution?
I also don't worry about an accident with these. The ink is a gel and not "wet" like marker or highlighter ink, where just brushing them against something leaves a mark. You sort of have to "apply" this ink where you want it.
Hopefully this little tip is helpful for anyone struggling with a color chart. Click on the "How To" label at the bottom of this post or the tab at the top of the page for more tips.