Well, it's sort of going to depend on what program you use for your digital art, I use Photoshop Elements 10. I probably color in the most inefficient way possible though, being, just like I color something traditionally. Using the paint brush and trying not to go outside the lines.
I make a new layer bellow the outline though and that's what I colour on, usually with some bright awful colour that I would never actually use in a picture.
After that I make another layer right between the outline and color and make it into a clipping mask using the little layer options in the top, left corner. That makes it so that whatever you do on that layer only shows up on the stuff you already coloured, so you can do stuff like complex markings and such with reckless abandon.
Most digital artists I know use the lasso tool to accomplish the same goal but for some reason mine's just a little too glitchy for that.
