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Calibre creates collections in your reader for everything you put in the Series and Labels fields in your books' metadata. Sometimes you don't even need to add anything, as most books include tags in their metadata that calibre copies to these fields.
So, after adding a book to the calibre library, right click on it and select "edit metadata". The metadata editor dialog will show up. Delete all series and labels information you don't want to be transformed in collections in your reader and only after that transfer your book to the reader.
In case you have already transferred the book to your reader, open calibre with your reader unplugged, modify metadata as desired and then plug your reader so that collection information is updated.
Hope this helps...
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