there's always a trial and error approach at the beginning when playing with a new device, especially one that can get corrupt so easily.
i only use calibre to transfer books to my kobo's main memory. i use ade to download the books from kobobooks that i purchase and then load that book from the my digital editions folder into calibre and load it onto the kobo like that.
you do have to be careful to eject the kobo correctly or you'll get a corrupt database for sure. i've had it happen a few times when i first started playing with it. finding a system that works specifically for you and your kobo will come with time and practice and knowing what you can do with what you have available.
as for putting books directly on the kobo i thought dragging and dropping just the epub and not the folder was the way to do it.
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