It can actually be much simpler using the Addon Organizer, which is used in the above process. There is a button option "Backup/Restore", and in those options a choice to "Export Library for external tool". Once you choose that option it brings up a box with a "1, 2 ,3 " option, #1 "Export Library to scenery.cfg" then #2. being a note to "Run External tool Keep this window open" (Here is where to run the AEC configuration), and finally #3. "Recover original scenery.cfg".
This is basically what Mark above is doing, just makes it a little easier.
I 100% agree - backup your original scenery.cfg manually even though Addon Organizer does it for you . . .