I would not recommend using a Sharpie. They bleed on fabric, making the markings less than crisp. I imagine markers would bleed too. Be sure to test anything on a sample before committing. Pigma pens are designed not to bleed.
Do you have black fabric and iron-on fusible handy? Why not create fusible black lines out of black fabric or any other solid colored fabric? Mark lightly with a pencil, then iron on the fusible mark. You could even sew the lines permanently in place, provided you have used a sew-through fusible.