I have a dual monitor setup, and I am using Ubuntu 12.04 LTS I have changed the positioning of the monitors several times, and now for some reason some of the windows open up off-screen (outside of both screens), Update Manager, for instance. How can I position the windows on one of my screens?

You can get the window back on your screen by using

ALT + spacebar

This would show you the maximize/minimize/ ... options. Click maximize and it would occupy your screen.

You can also hit "move" and then either your mouse or arrow keys to move the window to your current window.