Step 1: Lines
There's two ways to get the outline of a picture into your program: either scan it from paper, or draw it free-hand on the computer with mouse or tablet.
If your outline is scanned, you'll want it as clean as possible - that means erase the stray pencil lines, and adjust the contrast so that the paper looks as white as possible and the lines look as dark as possible.
If you are drawing the lines directly on the computer, I suggest you draw it on an empty layer, so that the "white" parts are transparent on the layer. Not a requirement, but can make things more convenient.
Keep in mind it's better to start out big - scan your drawing at a high resolution so you can work in detail. You can always shrink the picture down later. I'm actually working at about twice the size of the images displayed here.
Anyway, once you have the outline, you can choose to set it up in two ways. Both will turn out looking about the same, so it's up to what you feel like. One is to set the outline layer to Multiply, and keep it on top of all other color layers--that way it will show up as darker than all the other layers. Otherwise, you can have the outline on a Normal layer below all the other layers, in which case the colors you add will be on Multiply layers. Whichever setup you choose (or even come up with your own preference), just keep in mind that as a general rule, the Multiply layer(s) should be above the Normal layer(s). Here's a diagram that hopefully makes things clearer.
On a side note, there's no reason that your line art has to be pure black, especially if you're drawing it free-hand on the computer. Colored lines can add a different kind of mood to the picture, so try out some variations.