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1. Why they decided to go with the on-device organizational structure that they have is not known to me. In general, Amazon takes the "no access to file system" approach that Apple does, so it does not surprise me that the files on-device are stored in strange locations managed by Amazon and not by the user. So I'm no real help here.
2. My Fire HDX syncs almost instantaneously with my Amazon Cloud drive. However, you can tell it to sync by hitting up Settings>Sync and Check for New Items (the top option in Fire OS 4.5.1).
3. The Amazon Cloud drive is NOT like your traditional file directory that you browse on your Fire like you would on a Mac with Finder or Explorer on Windows. It is basically invisible, but sorts and displays documents based on type. So, you can create a "Stuff" folder in your Cloud drive that has pictures, documents, etc., in it and those will all appear in the separate categories of your Fire for things like Pictures, Documents, etc.. But in the Cloud drive they will appear to be placed in the folders that you put them in.
On the Fire, Amazon cloud drive doesn't really work like Google Drive or Dropbox or OneDrive. The directory structure is more or less transparent to the Fire, as it will be told what types of files are stored in the Cloud drive, whether it should care about them, and where they will appear in the interface.
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