My question is regarding the bottom section of the config page, do i also need to find the third party airport services in the bottom box and move them over to the bottom right hand box.
Those are the "Airport Services", and they have no relationship to jetways, or if the scenery has jetways or not.
The only reason for wanting to disable GSX Airport Services files for an airport, is when a 3rd party scenery comes with custom local ground vehicles that has been made specifically for that airport, which can be noticed by the presence of an "AirportServices" folder in the scenery package. In that case, you might want to remove the GSX Airport services to be sure you see the ones provided by the airport.
If you are removing GSX Airport services for a 3rd party airport that doesn't have their own, the only result is you will still see GSX vehicles ( coming from the GSX custom Living World file ), but their operator assignment will be LESS accurate, because it will based on the few global regions in the Living World, while with GSX you'll get a more precise assignment by airport, following the normal GSX rules.
Note that, none of this has any effect on "proper" GSX vehicles you call for your own airplane when you start the GSX menu: those will always be assigned following GSX rules, because the will replace the default ones ( looking like GSX, but still default nevertheless ) that have been placed automatically by the sim around your airplane when you start a flight on a parking spot.