Calibre can be used to transfer books to the Sony reader. If the book is DRMed then ADE will need to be installed and the reader authorized through ADE so that the reader can open the DRMed books. But you only need the Sony Reader Library if you want to buy books through the Sony Store. And even if you use the Sony Reader Library to purchase books, you can transfer them to the reader via calibre are using your file explorer.

To copy books using a USB cable connection and a file explorer, connect and locate the Reader in your file explorer. For example, my Reader shows up as drive H:, so I can copy books from my PC to the Reader by placing them in the following folder:

H:\database\media\books\