So this is what *should* be happening in Calibre to transfer books over (on Windows anyway). You plug in your Kobo, in a couple seconds you should see the Calibre jobs icon at the bottom right start spinning as it detects the device, and then what books on it. A Reader icon will appear beside your Library icon near the top left. You can then select books from your library and use the 'send to device' button to transfer them over. Once the transfer is done, you should see them in the list if you click on the Reader icon.
Where in this process are you hitting trouble? are the books in ePub format?
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