Thanks - I never like to offsite link without checking first
Ok, first of all following the instructions here and then running MakeRwys.exe will drop a file named MakeRwys_Scenery.cfg into your sim root folder
This file is a scenery.cfg file that contains all of your scenery including ones in the Add-on folder
Via "Run" or your preferred method of navigating a folder, go here: %programdata%\Lockheed Martin\Prepar3D v4
BACK UP YOUR SCENERY.CFG FILE - For the love of everything good, please do this!
Rename/move your original scenery.cfg to somewhere safe, and then drop in the MakeRwys_Scenery.cfg and rename it to "scenery.cfg"
Run the AEC configuration for Vector, it will now have access to & scan ALL of your scenery regardless of where it lives
Once you've finished scanning, applied etc, you can quit FTX Central
Move your original scenery.cfg back to it's original location
It's a bit of a fiddle the first few attempts, but after a while it becomes reasonably quick (and you'll probably want MakeRwys.exe for other things like external ATC software and similar stuff)
The vast majority of scenery and my traffic add-on I've manually set up and written the XML myself (A good chunk of my time at work involves interacting with XML) so hopefully I'll be able to chime in and be helpful - I think I've learnt more by doing and breaking things than by the rather sparse documentation from LM