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I have a Sony PRS-300, use Calibre, and have never installed the Sony software.
Calibre works well as a tool to manage ebooks both on the computer and on the reader. You keep your full library in the calibre library. When you plug in your sony (and are not running the sony software), calibre recognizes the reader and lets you copy books between the calibre library and the reader. Calibre handles books that are DRM protected, although in that case some calibre features such as format conversion will not be available.
Purchasing books isn't hard. Assuming that you aren't going to remove DRM, it suffices to install Adobe Digital Editions and buy books from any store that supports ADE (there are many of them). Although you have probably already done it, you must authorize your reader, which ADE can do. When you purchase books, they will be downloaded by ADE, at which point you can import them into calibre. Be sure to get the books in a format that the reader supports, such as epub. Caveat: don't have both ADE and calibre running at the time you plug in your reader. They will both try to manage the reader and will get confused.
If you are going to remove DRM (don't ask me how to do this -- google is your friend), then you can avoid authorizing your device with ADE. Instead, buy the books wherever you want, strip the DRM, then import the books into calibre. You are not required to buy from ADE-enabled stores. As long as you have a way to strip a given store's DRM, you can buy from there.
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