Ah, Doug, this is where it's all becoming so much easier.
Like I say, AFCAD files in the scenery subfolder of addon scenery, all other files in the scenery and texture folders of the addon scenery. Nothing need go outside in the main sim except things like effects.
BUT....wait for it. Once everyone gets to grips with XML and AFCAD and Airport (not too sure about FSSC...) have been updated to be full scenery design apps, there won't need to be any more separate AFCAD files.
Everything for a new addon scenery including navaids and stuff (you haven't seen my carriers yet) will go in a SINGLE bgl file so every addon scenery will just go inside addon scenery and have only a scenery and texture subfolder. In theory there need be only 1 bgl file in scenery (in practice there will be more files for other technical reasons I won't go into) but now you see why there is the move away from BGLC to XML.
Anyone who's installed Kai Tak in 02 and then in 04 will already have noticed how much simpler the 04 install was, and it's going to become simpler still.
Only problem is, in order to go into object libraries, all new objects will have to be created in GMax. I for one don't have the time to learn what is I think a grossly over-complex object design prog so I suspect my days in scenery design are already numbered. Maybe I'll then be able to get a proper life back!