Nearly every WWII training post with ~1000 or more people had a railroad siding or was situated near close rail access. Decisions to build the fields and camps was based on nearness of railheads for transportation of ALL materials- the interstate trucking system we depend on today was not developed anywhere near what it is today. Everything was moved by rail.
That said, most aircraft were manufactured, tested, and then flown to their destination of use unless they were to be shipped overseas. After that, if an aircraft had an accident that required higher-level overhaul than a base could handle, it could be disassembled and shipped for this overhaul at another location. However, with the scarce supply of parts in WWII, an aircraft which was beyond local repair capabilities might be cannibalized in place and some of those parts might be spread in the system to other bases. But those parts would have been very carefully crated and packed to handle rail or road travel.
I have O-gauge stuff (it's just for my kids, honest) and the way I would model this would be to put in a set sidings next to a crating operation. Where this would have been done was in base engineering section on the airfield- the aircraft would have been broken up, parts separated and crated, then shipped by rail or truck depending on how far they had to go. I just ran across this the other day when I was researching local military buildings. Just to the West of Marietta PA is a set of buildings which was used for this purpose in WWII. You can see the remains of the railhead where they loaded aircraft parts and pieces on the sidings between buildings- they were purpose built just for that operation.
http://maps.yahoo.com/#q=Marietta%2C+PA ... vt=s&trf=0Marietta Air Force Depot was a storage facility for aircraft spares which was part of Middletown Air Depot in WWII. My friend's father worked there until they closed in the late 50's. Middletown Air Depot is now Harrisburg International Airpot. The Air Force Depot in Marietta was probably more elaborate than what you would see near a training or air base in the South- down there, you are talking just a siding with maybe some platforms to make it easier to load large crates.
For other ideas, I would refer to Thole's books entitled "Forgotten Fields." There are lots of photos of how air bases were layed out in WWII, including comprehensive aerial views which will show the rail sidings on or near the base.