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Well (as a fellow Ubuntu user) I can offer some words of wisdom.
In terms of adding books you have a few options (I don't own a Kobo so I might not list them all).
1) Use ADE (you are having problems with it and not wanting to pursue this method, so we'll scratch that one.
2) Plug the Kobo in and Ubuntu should mount the reader. From here all you will need to do is drag'n drop the DRM-free epub to the Kobo, unmount it and away you go.
3) Use Calibre. Calibre is essentially a piece of software that keeps a copy of your drm-free ebooks, converts them to various ebook formats, pulls down metadata and the like....and copy the ebooks to your Kobo.
I would start with option 2 to get a book on your Kobo to get you going and experiment with Calibre.
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