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Originally Posted by Ashjuk
I have just added two books to my Kobo using Calibre. I installed the KoboUtilities plugin and I see that in the process they have been converted to kepub (title.kepub.epub)
I had created a folder in the Kobo memory as a place to store my books (Books) and by dragging-and-dropping I am able to put all my books there, and in various sub-folders, but I see Calibre has added them to the main memory each one in its own folder. So far I have been unable to find a way of automatically putting them in the 'Books' folder and if I drag them there it rather defeats the point of using Calibre in the first place.
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You can turn the auto convert off is you wish. I'm not at home right now, so I don't remember where.
Also, I'm pretty sure you can tell Calibre where you want your books placed. But I never bothered. Calibre sends all my books to the SD card in the Aura.
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Seems like there is a lot more to learn 
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There is. But as you can see reading this thread, it is up to you. You can drag and drop to your Kobo, use Calibre, turn all sorts of options on or off. You can patch the software to behave differently or install completely different software.
It all just depends on what you feel is worth your time.