Well, if it's just the issue of not wanting the menus over the scenery, you can undock the GSX Window and move it to another monitor on the same computer.
Note the menus are the standard Simconnect ones so, which means they all respond to keys (0..9), and GSX itself has a configurable hotkey too (defaults to CTRL+F12) so you could use macro programming on a keyboard/joystick to operate it without using the mouse.