It shouldn't necessary to disable Traffic X each time you go into KJFK.
Since they are referring to something in the scenery library, it's surely the AFCAD they provide with the package, which are probably made for the default KJFK, so it will not match with our KJFK.
If you find which .BGL in the Traffic X scenery folders controls KJFK, by removing it, you can keep Traffic X active all the time, because their AI airplanes will use our own AFCAD instead.