When you use a 3rd party airport, you should use the GSX Config options in the FSDT Installer, and use the "Detect 3rd party" button to exclude all 3rd party airports from jetway replacement, which is really only designed to replace jetways at default airports (hence the different positions ).
This is quite different than what we used to have in P3D + SODE + GSX L2, you can't just replace jetways for 3rd party airports with GSX and choose their model or position. Here, we have a set of about 900 .BGL file which contains only jetways, but are supposed to be used for default airports, because that's the data used in those files. So the exclude 3rd party jetway button, is there to prevent double jetways and wrong parking positions.