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Can't help with all your questions, but I can tell you that you don't have to choose between Reader Library software and Calibre. The two co-exist very nicely. You need some form of ADE (Adobe Digital Editions) to download purchases from the Sony store (or from other vendors that sell DRM'd books). If you have Reader Library set up, all your ADE purchases will show up in there.
Calibre is handy for making changes to the tags, and generally managing your e-book library to a greater level of detail than you can do with the Sony software. I normally download purchased books to the Reader Library, then add them to my Calibre library, where I adjust the metadata, tag them ("read" and "not read" for instance) and then upload them to the Sony Reader. I also use Calibre to remove books I've read from the Sony Reader as needed, while keeping copies on my PC for reference or if I should decide to re-read something. (I really don't feel the need to always carry hundreds of books with me on the Reader, especially those books I read but wasn't terribly impressed with.)
But as you play around with Calibre, you'll find your own ways to organize your stuff and shift between your PC files and your Reader.
Cheers,
Bev
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