As explained in the product page, GSX works with ANY FSX airport, both default and 3rd party, even those that aren't even released, the only requirement is the scenery has a correct AFCAD with no errors. Other than that, you don't have to do anything special, it will just work.
With the included Scenery editor, you can customize any scenery even further, to specify parking radius sizes and vehicles placement, so you can fix any possible problems like overlapping objects, which might happen more frequently with 3rd party sceneries, that are usually more detailed than the default ones.