Once I've cleaned up the line art with the pencil tool, I have to set up the layers. Right click the Background in the layers menu and select Duplicate Layer. I usually give it a name (like "Line art") by double clicking on the new layer. I then set the blending mode on the line art layer to Multiply (Burn) by choosing it from the Mode drop down menu on the layers dialog while the line art layer is selected. This causes the black lines to stay opaque while the white becomes transparent (so you can color beneath the line art). I then select the Background layer again and fill it with a light color (filling it white sometimes leads to mistakes in color choice and leaving areas uncolored). Simply choose a color and hit Ctrl+, to fill with the foreground color. I then create a new, blank layer between the two to fill in the colors. Just click the icon of a blank page in the layers dialog. At this point, my layers look like this:

With my layers ready, I now begin to lay down the base colors. This is done by selecting portions of the image with the magic wand and the bezier selection tool. The trick to using the bezier select tool is to complete a shape, and then double click inside the region to make a selection with it. It is often helpful to expand the selection (Right click, then Select > Grow...) a few pixels when using the wand, so the selection will go under the black lines. It is important to have the selection's edges remain under the lines so no edges in color are visible where they shouldn't be. To add to a selection, hold down shift and make a new selection. Similarly, you can hold control to subtract from a selection. Once I have an area of common base color selected, I fill it in the color layer with Ctrl+,, and move to the next area to begin selecting again.