I'm a little confused by your workflow. Maybe if we answer these questions then somebody will be able to help you better.
1) Do I understand correctly that you are buying the books from the Sony ebookstore through Reader Library software? Yes & also from Smashwords
2) You have made your own collection names in the Reader Library software, yes? No, on my Sony350.
3) Do you use the Reader Library or calibre to transfer the books to your ereader? At the moment I am using the Reader Library to transfer to my reader.
4) Your post says that you transfer to calibre from your 350. I am not sure why you do that? Did you maybe mean the opposite? That you transfer from calibre to your 350? No I am slowly transferring all my books to Calibre for sorting & storing them (from my Nook, Kindle & Sony). BUT if it would make more sense I will use Calibre to download my books to my 350.
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My concern is that even if I download one book from the Sony store to my reader via the Reader Library, It causes my 350 to make over a 100 collections based on tags & then putting that one book into each collection created. Now I'm not sure why it is doing this.
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