Scott Chacon, author of Pro Git, gave an interesting talk at Strange Loop entitled A Tale of Three Trees. The idea is to understand how Git works by understanding how it manipulates the three trees: head, index, and working directory.
The talk is a little over 45 minutes and worth a look. It will help you understand some of the fine points of Git. If you do watch it, don’t view it full screen as you won’t be able to see his slides that are displayed in a secondary window.