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If you are new to Kobo and you like configuring every thing to your preferences I would recommend loading a few books at first and testing different configuration options. I think with a lot of books the special Calibre plugins to manage the library can be handy. One to automatically assign books to shelves, and another to backup your Kobo database so if it gets corrupted, you can restore a backup and get the majority of your books on their shelves.
The plugins may take some time to configure toyour liking, so that's why I recommend try ing first with a few books.
The pluging names are Kobo Touch Extended and Kobo Utilities.
Learn about the differences between epub and kepub format, so you can use the one you prefer
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