I don't know what you mean by "GPS only".  If you followed the installation instructions properly and cut & pasted the folders into /ADDON SCENERY you should have seen the "recreating scenery indices" notification the next time you started FS.  As the instructions state, each carrier has a VOR and ILS, although, for some reason, they won't integrate into FSNavigator.

When you click to load it up FS always takes you to the default airport.  You might be able to create a flight that starts on a deck but you have to get the altitude perfect.  If you're off by one foot you will crash into the deck.  I created my carrier flights by landing, lining up for takeoff, then saving the flights.