I am using Xcode 3.2. How can I add more ViewControllers when I make them via “new file” to the MainWindow panel in the Interface Builder. For example, in this picture the bottom 2 squares are there by default. How do I add similar ones to represent the new ViewController(s) I just added.

You can only have 1 view controller per nib. Create a different nib for that and any other view controllers you want, or start using storyboards (which requires you to update Xcode).