I've been using mostly
Calibre and love it. Most of what I've loaded are epubs and pdfs and some old Kindle format files I collected over some time, and it will convert from any format into what you need. I've also just dragged and dropped books onto the 350 before I got more organized with Calibre, now I use that exclusively. There's also a
forum section right here for Calibre if you have any questions at all about it.
I'm pretty sure I also used the Sony software at first to transfer over some books, none of which I purchased from the Sony bookstore.
Hope you enjoy the Sony 350 as much as I do, I just love mine.