Right, first things first, scan your image as a greyscale or RGB image, you can scan an eight bit indexed colour image but you'll need to convert it to RGB or greyscale for the next step.
Clean it up as you feel fit, I use the Levels or Curves tool to adjust the blacks and whites. Once you've done that make sure your image is in RGB mode, if it isn't already. If you're working on a hight resolution image i.e. one intended for print there's a tip make life easier on machines with limited resources, see note 1 at the end.
Now create a new layer on the image and use the channel to perform a selection .
Now perform a fill operation with black as your colour, you may have to invert the selection first, as black is normally the default mask colour for channels.
Now create another layer and move it beneath your outline, perform a select all and fill it with white.
Congratulations you've now separated your greyscale image into two portions, it's useful to name each layer as you go along, I suggest Outline and Base.
I generally perform this step using white and then set the opacity of this layer to some percentage.
- First set the active layer to the one you painted in your lighter flesh tone on.
- Perform an alpha or transparency selection so that coloured area is the selected portion, in Gimp this is: Layer/Transparency/Alpha to Selection.
- Expand that selection, the amount you expand it depends on the resolution, some where between 5 and 12 pixels works for most screen resolution images, in Gimp this would be: Select/Grow for the appropriate dialogue.
- Now Feather your selection, this step is optional but you'll probably want to do it, the amount of feathering is resolution dependent, something less than half the amount you grew it is about right.
- Invert your selection.
- Set your base flesh layer to the active layer.
- Perform a selection intersect with the transparency on this layer, with your current selection, in Gimp this is: Layer/Transparency/Intersect with Selection
- Create a new layer, name it Flesh Shade.
- Perform a fill with your desired flesh shade colour.
In most cases, I like to perform this step with a solid colour, in this case a blue, then use the layer transparency to moderate it. If you're using it for a reverse high light, you'll need to keep the colour solid.
The image in context, funnily enough I'm not happy with the face on this so it'll probably be changed pretty soon.
Note 1. Human visual acuity is concentrated in black and white, so you can get away with low resolution colour as long as the tonal range is in high resolution. If you need to create high resolution images in can be easier to colour them at low resolution and then rescale them and add a high resolution black overlay.