The main window is called the Program window and is often just referred to as the timeline. Here is where you enter the main menu operations. This timeline consists of a vertical stack of tracks with time represented horizontally on the track. It is the output of the rendering operations and this is what is saved when you run the File pulldown, Save command. Immediately to the left of the timeline is the patchbay. The patchbay contains options that affect each track. These options are described in great detail in The Patchbay.
The Window pulldown on the main window contains options that affect the 4 main windows. The first 3 options are used to display each of the windows in case one was accidentally closed. You can move or resize the windows as needed, save that particular layout, and revert to the default positions to reposition all 4 windows to the original screen configuration. On dual headed displays, the Default positions operation only uses the one monitor to display the windows, but as you can see in the Window pulldown you have more options to change that with the 2 tile options. Usage with dual monitors is explained in Playback A / Playback B.