Dying nylon// "tactical" gear.

Have you tried to remove the sharpie marker from it first? Test a small location inside to make sure you aren't taking the coloring out of the condura first, but nail polish remover or cheap-ass pump hair spray (white rain I think is one of the brands) will dissolve the ink.

Rit dye will work. The water should be very hot.

I would also try removing it first as well. If you don't you still might see it after dying.