I use both programs. I recommend that you try them both and see what works best for you. I prefer the Sony Reader Library software for managing my books. To me the Reader Library software is similar to iTunes. I keep about 600-700 books on my 950. I have them organized into dozens of collections, which are just like iTunes music playlists. I like that I can order the books in my collections however I like (not just by author, title, date). Then, I can auto-sync my collections on my computer with my ereader. I can also keep notes on my ereader or the computer and have them merge together. Since I read a lot of library books and purchase books through the Sony store (so I have to use the Sony software anyway), it is just convenient to use it for my whole library. For whatever reason, the Reader Library seems to work great with some computers and not so well with others.
I use calibre for file conversions and to edit metadata (I especially like its ability to use internet databases to download book summaries and covers). I also use it for my non-DRM books to customize them with fonts and paragraph formatting to my tastes. I also love calibre's Fetch News feature and its ability to create ebooks from internet news sources, magazines and blogs. Calibre seems especially popular with people who have lots of books that are part of a series.
Really, I think the best advice is to just try them both. Hope that helps!
