You should have trusted the installer, instead of panicking and assuming it did something wrong...what the installer does is:
- It will ASK you for a location. Big improvement over the old version, which *forced* you to install into the root of the sim. Users have been asking for this for years, especially those with the sim installed on SSDs with not so much space left. Now, you can keep the sim and the sceneries even on different drives.
- It will MOVE all your FSDT and Flightbeam (only the ones requiring the Addon Manager) to your newly chosen folder. Even if you now have complete freedom in choosing the destination folder, our stuff MUST still stay together, all in the same folder. They are designed to be like that, and it makes for easier updates too. So, in order to SAVE you from Uninstalling everything, Downloading all the new installers, and Reinstall everything, only to get the same files just with a new installer, the installer save you from this, and it simply MOVED all the FSDT/Flightbeam sceneries to their new location, the one you chose freely in the first step. Nothing has really changed here: the sceneries were all still together in the FSX\Fsdreamteam folder before, they still are now, inside a folder of your own choosing.
- Another big improvement that, before, if you had several versions of the sim, for example FSX, P3D 3 and now P3D4, you were installing the same scenery 3 times, wasting a lot of space. Now, the folder is shared between all sim, not wasting any disk space, and make it less confusing for updates, because when you update a scenery, it will be updated for all the installed sim.
In any case, now that you are free to install everywhere you like, choosing the SIM folder, it's probably the worse possible choice. If you have enough space on C:, the proposed default location the best one, so you have all our stuff in its own folder. You cannot be any tidier than that.
If you want to use another drive, just select the root, and it will install everything into an Addon Manager folder under it, like D:\Addon Manager. This is also a perfectly fine choice.
About scenery rearranging, the installer doesn't do anything different than it used to: it will always place the last installed scenery in the topmost position. Nothing new here, since airports should always be on top of everything else. So, if you used a 3rd party utility to rearrange the Scenery Library after everything is installed, it's ok, as long this utility doesn't corrupt the scenery.cfg (some of them do). This is for FSX only. Under P3D 3.4 and 4.x, we don't use the scenery.cfg anymore, so you'll need specific utilities made for P3D to rearrange them.