Painting from reference - use image as base or start from scratch?
I would personally paint it separately from the original drawing, for a few reasons:


I find that if I paint over pencil using acrylics, either the pencil lines become completely obscured by the paint such that I can no longer see fine details (such as shading), or for thinner/lighter colored paints (such as yellow), the graphite mixes in with the paint and muddles it.
Plus, you may want to paint on a surface that is more suitable for painting on than drawing paper, such as heavier-weight paper (mixed media or watercolor paper), canvas board, canvas, etc.
This would also allow you to keep your reference image separate from the painting, in case you change your mind with how you decide to paint the image.


What I would recommend doing is to very lightly draw just the general outlines of the image onto another paper/canvas/board for painting. If you have a kneaded eraser, it would work really well for lifting some of the excess graphite so that it leaves just the slightest trace of the line behind. (If not, use a good eraser to very gently remove some of the graphite, without smudging.) Then begin painting in the medium shades, then shadows, small details, and highlights.

Hope this helps! If you have any questions, please feel free to ask.