If you want a good super basic way...
Scan your pencil drawing.
Layers Palette:
(Assuming it's the background layer) double click on it. A dialog box should open asking you to name it 'Layer 0'. Click OK.
It has now become an editable, movable layer, just like all the others.
Layers Palette:
Where it says 'normal', change it to 'multiply'.
Layers Palette: Create a new layer. Make sure that this layer is set to 'normal' and not 'multiply'. Reposition it under 'layer 0' by grabbing it and dragging it to the bottom of the layers list. Do your coloring on this layer.
You can create as many separate 'coloring layers' as you like and edit them independently. It's usually best not to color on your original lineart, but instead, turn it into a transparent layer using the 'multiply' mode.
If you want to learn a more complex method of coloring, this is a good way to learn:
http://www.melissaclifton.com/tutorial-lineart.html