I just received my H2O and copied epub files using the file manager. I'll dig into Calibre next week. I'm running Ubuntu MATE 16.04 and when I plugged the Kobo into the computer it was recognized as an external drive. After I clicked on the Kobo in file manager I pressed CTRL + H to show the hidden files then I created a new folder called Books. I pasted the epubs in to the Books folder then clicked the Eject icon on the left side of the file manager. The H2O said it was disconnecting then a processing message popped up. Once the messages went away I browsed to the library and there were my books.
Good luck.
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