Regarding the scenery/aircraft locations, here's how they have been reorganized (I hope this clarifies things):
- aircraft downloaded from the Aircraft Center and TerraSync scenery are saved in <download location>/Aircraft and <download location>/TerraSync, where <download location> can be set from the Add-ons tab of the Qt launcher (it's ~/.fgfs on Mac/Unix system and C:\Users\<your user name>\Documents\FlightGear on Windows, if I'm not mistaken). Thus, the download location you specify in the launcher is not just the TerraSync directory, but rather a directory containing both the TerraSync and the Aircraft download paths;
- additional scenery and aircraft locations (which will be not automatically updated) can be specified in the Additional scenery locations and Additional aircraft locations panes, if needed.