I use Rapidographs, India Ink, Watercolors(paint or pencil), and Acryllic in conjunction with eachother all the time. Each are not waterproof.. so watch the saturation of your materials.
When you get something reproduced, you want to have them produce it on a paper that is acid-free, or an art paper that you can manipulate further etc... and not have to worry about the paper yellowing over time.
Most giclee printing facilities are aware of this and account accordingly. But is good to ask, and be in the know.
I had a similar situation that you are contemplating with a set of Geisha's I did in Black & white (Pen/Ink) and I wanted to add color etc... I decided to have them reproduced on a heavy watercolor type paper, so I could retain my originals as they are... and I painted color on the reproductions, making them originals in their own right.
A less expensive route is have your image scanned, and do all color saturation via a digital program (Photoshop if you already have it) or a like program. (free/shareware or otherwise)... If anything, its a good way to satisfy the curiousity of knowing whether or not you want to 'go there' with an actual painting/drawing, etc... or on reproduction as I described above.
Hope that helps.