Before I color, I make the background a neutral color other than white, such as a tannish brown, or the blue you see below. I then create a separate layer for each color, and label them appropriately. In the layers section in the bottom right corner of the screen, you can see the layers for "Beads," "Scabbard," "Inu Kimono" and "White Stripe." There are a ton of other layers for hair, eyes, skin color, etc. that aren't visible.

I then lock each layer and shade each color the same way non-virtual artists would use oil paints (I think, anyway. I sucked the few times I ever tried painting with oils). For shading, I use the airbrush tool and set it to 12% pressure for the drawing stylus. I use various brushes for different effects, such as the speckled brush for the hair shades and highlights.