Amazon just released the first version of their Windows app to sync Amazon Cloud Drive. It’s very much a first version, with no ability to pause/resume sync, sync selective folders, or even (as far as I can see) a way of changing the default sync folder.
It chose the smallest drive on my machine (of course), but I found a way to change it.
Do this entirely at your own risk, and if you don’t know what this means, then don’t do it. You can use regedit to change the sync folder’s location, under "HKEY_CURRENT_USER\Software\Amazon\AmazonCloudDrive\SyncRoot" change “SyncRoot” to a different folder.
Works for me, but no guarantees.