I'm sorry but, I don't really know how I could have explained it any better...
Yes, of course the default configuration we made for the PMDG 747 doesn't have any of the 4 possible passenger doors to play the role of the upper deck door. YOU must edit the default configuration that comes with GSX, and set one!
Yes, it MUST be one of the 4 passengers doors. GSX doesn't handle more than 4 passengers doors in total so, if you want to use one of them as the upper deck door, you must edit one of them, and move it on the proper location IN THE 3D EDITOR. The one that would be more suitable for this would probably be the Passenger door 3.
Just edit the Passenger door 3 with the 3D editor, and move the arrow on the upper deck place. The diagram won't change, of course, but it's not a problem. As long as you use a passenger door (you cannot have a cargo door to play the role of a passenger door), it can be everywhere on the left side of the airplane.
In addition to that, you will probably have to edit the custom XML expression to change the name of the variable that controls the door, which will have to match the one that controls the upper deck door. Or, just set the door to have no open/close checks, so GSX will ignore if it's opened or closed.