It's impossible to help you with such a generic description of your problem. GSX surely reads the correct AFCAD and it respects both the layer priority in the scenery.cfg and the one in the add-on.xml files.
You haven't even said which simulator you use, so I cannot even tell if the add-on.xml file is relevant.
So, please, describe your issue more accurately, like which scenery you use, how they are layered, which simulator you use, etc.