To use your scanned image as an outline and keep it above do the following:
Import your image. Create a new layer. In the layer stack, drag the new layer to beneath your scanned image layer.
In the layer stack set the Blend Mode of your top layer (the scanned image layer) to be 'Tint'.
Now select the lower layer - the new empty layer - and colour on that. The black lines of your scanned image will stay black, but the white paper colour should become transparent.
If you dont like working against transparency, you can edit the paper settings of your lower layer to make the paper opaque.
Note that you can also set the paper roughness to be 0%, so the tools you use will give more solid colour without breaking up from the paper.
AndyRage's mantra for graphics engine code:
"Sure - how hard can it be?"