Doug,
maybe the three pictures below can explain a little bit how alpha channels work. They are like masks. You can use them to create cutouts or for filter effects which should only be applied to a specific area of the picture (in this example, only the white area gets cut out). white means 100% effect, black no effect.
In my ccf (glad you like it) I used Photoshop only to convert it to the Prontoscale or to cut the buttons out of the pictures. (I used alpha channels for that, too ;-) ) The main work was done with 3D Studio Max, which I can use at work. Fortunately.
André