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"Extracting Lines onto it's own Layer."
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This 'lil tutorial will show you how to take a sketch/drawing and ready it for digital coloring. I'm using Photoshop CS for this tutorial. Should apply for other painting programs that allows layering & channels. Alrighty then, begin by scanning & importing your image into Photoshop. Here I've imported my sketch (A Garm concept) into Photoshop. Note: I used a red pen. Doesn't matter what color/medium you use for the sketch in the end it'll be black (or what ever color you want :P )

I start by messing with the image's Levels (Images>Adjustments>Levels. Or CTRL+L). Play around with the 3 triangle tabs til you're satisfied. Bottom two tabs are the images's overall white / darks.

Once Level-ized :P Click+drag the background to the "Create new layer" button. This will give us a new copy of the sketch, "Background copy". Select "Background" and fill it with white. Select "Background copy" (Rename if you'd like) and click the "Load channel as selection". What this does is select all of the whites of the image. Hail the marching Ants >.<

When the ants appear, Hit Delete. We have deleted eveything white in the image. You'll notice the image is now faded. No problem. Lock "Background copy's" layer.

Now fill the whole image with black (ALT + Backspace fills with Foreground color, CTRL + Backspace with Background color.), or any color you want your lines to be. In the example, I chose black. Left side shows the result. It's still a bit faded, so I duplicated the layer (Right side).

And that's it. The sketch's lines are now on it's own layer. You would just create a new layer named "Color" and paint away :P Top left = Black lines. Bottom left = Green lines. Top right = Red lines. Bottom right = Blue lines.

And if you were wondering, the layer set-up for the above's example.

Another way to have your lines "above" eveything is to have your "line drawing" (Works best if it's a black & white image/sketch) on the top most layer, and change it's blending mode to "Multiply". This may be quicker/simpler, but I've found to have less control over it. That's all for "Extracting Lines onto it's own layer". To top of the page.