You can use RIt or Tintex dyes found in supermarket and fabric stores...for the most part they do a good job. The only problem is that in some colors they do not have the intensity of aniline dyes. Particularly the reds. Blue, green and yellow are all available in intense shades.
Hobby craft stores specialize in cottage industry type fabric dyes: aniline colors called Dylon(?) and they work quite well.
Rather than use a Sharpie marker, try using silk fabric paint which has the consistency of white glue or paste and dries quickly, never "bleeds' and they make some specifically for silk which will NOT cause the fabric to become stiff. It's only a few $$ to try it out!