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I don't really use the sony software much, but it is really easy to make collections with calibre. Every tag you add to a book becomes a collection. A book can of course belong to more than one collections at the same time.
I like epub, and I usually convert to epub if I have to choose. I haven't given it much thought, so I can't really say why I like it more than lrf. The page numbers on the side can be just a little bit annoying sometimes, but I don't mind the left justification at all. I actually prefer it from full justification.
Good luck with your grand experiment, Daffy!
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