Placing various effects or bits of footage in front of or behind one another is what layers are for, and they work just like if you were stacking papers: The layer on top will be in front of everything below it. This knowledgebase article
explains the layers system a bit.
For cases where you can't just change the order of the layers, you use masks to simulate one layer being behind another. This knowledgebase article
explains how masks can be used for this purpose. So does this video tutorial.