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Series is designed to do exactly what you are trying to do. Series is the name of the series. Book identifies where that book appears in the series. So when entering, say, Harry Potter and the Prisoner of Azkaban into metadata, you might choose Harry Potter for the series, and 3 for the book. In the main Calibre display, you get Harry Potter [3] for this book under series.
If you send the entire series to your reader at the same time, you end up with a collection called Harry Potter with the books organized in series order inside that collection. I believe that if you send them over piecemeal, they still all show up in the right collection, but not in order.
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