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The best setup really depends on user preference. The two choices that I'm aware of are collections and folders. Folders is just like it sounds. Your computer sees the reader as an external drive and you organize books to suit yourself. The plus is that things are exactly where you want them. The minus is that if you want to find the book in multiple folders, you have to have multiple copies.
With Collections, the books are grouped by metadata. If you use Calibre to manage your library, Calibre will use the tags and series information you give it to put books into collections. You might have the book in multiple places but they all point back to the same copy. The plus is that if you have good metadata and Calibre, this is all handled for you. The minus is that you can't select based on two separate tags at the same time. If you want to find a book that is historical fiction and a mystery, you have to look in historical fiction and try to identify the ones that are mystery books. I have readers that work both ways and I like both systems for different reasons.
I would suggest narrowing down to whether you want folders or collections and then looking at the readers that have your preferred organization. Also, look at the ergonomics of the reader. You have to turn the page a lot to read a book; if the controls are not in good places, that can become painful.
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