It's good to see that Layers Magazine finally began offering Premiere Pro tutorials about six months ago. In this tutorial, Franklin McMahon demonstrates the uses of media created within Premiere Pro.
The tutorial demonstrates how and why to use transparent video in your timeline. Also note that in Premiere Pro CS4 color mattes support an assortment of blending modes which opens up some visual possibilities. (Here's a link to information on blending modes and what they do.)