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I think it's a great idea to start to get familiar with Calibre, and to start learning how to manage your shelves with Calibre. If you start by putting a lot of effort into organising things like shelves directly on your device, you may get a rude shock if you have to reset your device and lose all of that work. Setting up shelving (tagging/collections/whatever you'd like to call it) in Calibre means that you can very quickly and easily restore all your organisation with minimal effort.
There are also some terrifically useful plugins for Calibre: KoboUtilities, for example; and if you'll be buying DRM books, befriending Apprentice Alf can be helpful also.
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