The scenegraph serves 2 main purposes: keep track of the relationships between the various windows and act as a window manager for them.
You can press F3 in the primary console, the floating paint palette, or any one of the viewports (plots or non-modal dialogs) to raise the scenegraph to the top so that it's not covered by any other windows. The window over which you press F3 has to have the focus of your windowing system. In general, clicking the title bar of a window or any place inside of it will make it the focused window.