Yeah, any newly transferred epubs you load on the Kobo should appear as 'NEW' on the I'm Reading list.
HOWEVER, if you do not open them by the next time you plug in your Kobo, when it processes after unplugging, 'NEW' books get filed away in your library (taken off the list).
@TIM:
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However, it may be possible modify the GUI to allow you to add a book on the device to the reading list. I have not looked at it yet but it might be interesting...
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Personally, I would be more interested in exactly the opposite of this; Taking books on the I'm Reading list and filing them safely in the bookshelf.
Although I don't really know how you would accomplish either using the Calibre GUI. Is Calibre extensible to the point of allowing you to add/modify the context menu so we could do this via right clicks of books on the device list?