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?
2) You have made your own collection names in the Reader Library software, yes?
3) Do you use the Reader Library or calibre to transfer the books to your ereader?
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?
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