Today's comic gives me an excuse to show you how I do that dark effect in my comics.
Firstly I color the comic normally as if it's all in broad daylight. I then fill a new layer (in Photoshop) with my dark color, set the layer blending mode to 'multiply' and simply erase the areas that I want the light to shine through on. This is fantastically satisfying to do.
This method also gives me the advantage of already having the dark part completed for when I do the gray/bw version.