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Kobo will process any / all files present within regular directories on either the internal storage or the external SD card. So since you copied three files per book to the storage (epub / pdf / jpg) it will process and add ALL of those to it's database.
If you use calibre, with the device attached to your Mac you would just send the desired material to the device (ie more than likely just the ePub) (either to main memory which is the internal storage or memory card A which is the external card), and if you desire, the cover.jpg can also be sent, but not to the same directory as the ePub; rather to the "hidden" directory where Kobo stores the images it would normally extract from the ePub itself.
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