When you buy a book it automatically goes to your library (on the dot com site) in my experience.
I have also been told to plug in the reader before opening the desktop app (make sure ADE is closed as well) and when your desktop recognizes that the reader is there then open the desktop app and you will see the "sync" on the LEFT side. Click it and it adds anything new added to the library.
I have not lost my place in what I am reading when I do that.
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