Every GSX .INI customization file works ONLY with the AFCAD it was made with, and you can check which one is by looking at the [General] section of the .INI file so, there's no risk of adding an .INI file and using it on the wrong AFCAD, unless the AFCAD has the same name, but has been changed/updated in a way that it won't match the .INI anymore.
And no, don't worry about the full pathname you'll see in the .INI file. As explained in the GSX manual, this full path is used only as a reference to the .INI author to help him recall where the scenery was installed on his system, but GSX will IGNORE the path and will use only the bare filename. That's how you can exchange .INI files with other users: as long the active AFCAD name matches the name referenced by the GSX .INI file, it won't matter *where* the scenery is actually installed.
For 3rd party sceneries that have multiple AFCADs to choose from, you will need a separate .INI file for each one. If the difference in the various AFCAD are trivial and not related to GSX (for example, different runways active depending on wind), you can usually just make a copy of the first .INI file, and change the AFCAD name to match the alternate one, and they will switch automatically in GSX when you switch the AFCAD, provided you follow the naming convention that the first 4 letters of the filename MUST be the ICAO code of the airport, while the rest after the dash can be everything else.
