Now that you have your lines on their own layer (and therefore protected from coloring), select the color layer.

Using the lasso tool, select the individual parts of your image. (In this example we chose her skin, hair, dress, and boots, one at a time.)

After making a selection, fill* it with a dark shade of whatever color you want,then save it as a channel by pressing "Alt+S", then "S". This will bring you to the "Save Selection" screen, where you can just hit "Enter" to save the selection as a channel.

By doing this, you are preserving your selected area for future use. This will save you a lot of time, instead of having to re-outline your selections over and over. All you need to do to access the selection, is to either "ctrl+click" on one of the channels, or press "Alt+S" then "L" to go to the "Load Selection" screen. (You should mess around with this for a while, just to get the hang of it.)