Have you thought about applique? You could fuse black material where needed and then stitch around it to secure it. I don't know about Sharpies.
I just checked the Sharpie web site and here is what they say, "We also do not recommend the Sharpie for use on cloth as it may fade or bleed in the wash. Also, over time a yellow halo may appear around the marking."
Ask at your LQS or fabric store if they have any permanent markers.