Terminology is the first thing to understand, so people know what you're referring to. "Autogen" is a term for buildings, objects, and vegetation that are placed using the annotator tool. Most anything you find on the airport grounds is not autogen, but custom objects. Autogen is the filler that covers the ground elsewhere in the sim, outside of airports.
Custom objects are single objects, such as hangars, static vehicles, etc. that are either designed from scratch by the developer using Gmax or some other 3D modeling tool, or called from a library of existing objects within FSX. They're placed in the sim using a placement file that's compiled by the BGLComp.exe tool. Generally, the buildings at an airport are done this way.
Then you've got your airport facilities file, commonly referred to as an "AFCAD", which contains the airport layout, including runways, taxiways, aprons, and flatten/exclude switches.
The first thing you want to do when redesigning a stock FSX airport is to create a new AFCAD file. My favorite tool for doing so is Scruffy Duck's "Airport Design Engine" (ADE), which is freeware -
download it here. I suggest you get a copy of ADE and read that manual. That'll at least get you started.