First, be sure you understand the difference between customizing the *parking* position (which is the position/rotation of the Parking spot ITSELF), and the *stop* position, which is the position GSX expect your airplane should end up when parking, used by the GSX Marshaller and the GSX Docking system.
The parking position is customized by clicking the "Customize Parking" button, and it's shown in the 3d editor as a large circle centered around the airplane, which becomes orange if it's active. If the large circle is orange, you know you are editing the *parking* position.
The Stop position is customized by clicking the "Customize Parking System" button, and it's shown in the 3d editor as a much smaller circle, that becomes orange with a "STOP" sign on top of it when it's active. If you see the stop sign, it means you are customizing the Stop position.
The parking position customization is used to fix in GSX any possible issue with the parking position/rotation/size in the underlying AFCAD without having to change the AFCAD itself. This only affects GSX, the simulator itself (AI, the standard "Go To Airport" menu, etc.) will continue to use the original data in the AFCAD.
The stop position customization is used to tell precisely where the airplane should stop, and it takes into account the preferred exit, as explained in the manual on the chapter "Understanding the Stop Position". This data is also used only by GSX Marshaller/Docking systems to know when to stop, and when you place the airport on a parking Using the GSX Menu.
That's why you probably got confused: if you used the standard World -> Go To Airport command, the simulator will continue to place the airplane center of mass in the center of the parking, as defined in the AFCAD. The simulator itself doesn't know anything about your GSX customization, so it will continue to use data from the AFCAD.
Instead, if you want to jump to a parking and being placed were GSX expects, you will have to use the GSX menu with the "Warp Me There" feature. Since this is a GSX feature which can basically replace the standard "Go To Airport", it knows about your GSX customization, and will use it.
And, as explained in the manual on the stop position chapter, if you customized the parking with some kind of airplane model and you'll later use a different airplane, GSX will position (or will expect you to park) the new airplane using this strategy:
- The airplane in use will be positioned with its Preferred Exit lined on the same position of the Preferred Exit of the airplane used to customize the Stop Position, which will likely result in the front gear in a difference places, exactly like in reality, since the goal is to have the Preferred exit always in the same position, in order to move the jetway as little as possible and to be fairly sure that, if a jetway worked on the plane used to customize the parking, will likely work on a different airplane.