It's your responsibility to place the right jetway model in the right position, in order to have the expected result of resolving the aft jetway on the 2nd door and the fwd jetway on the 1st door.
GSX won't prevent you to cross jetways. You only have to play with the editor, choosing the right models and positions. That's why we have so many too choose from. And of course, the parking stop position does have an effect on this, and that you can customize too.