Sony wrote a PC/Mac app that you can use to support your Sony Reader. Unfortunately, it doesn't work too well.
There's a checkbox you can select in the settings that will menu have the PC app sync your reading location and annotations from the Sony Reader to the PC. But if you click that box you had better not ever unclick it; the app will take it as a sign that you don't want the ebooks any more.
They will be deleted, but not just from your computer. The app will also delete the ebooks from your Sony Reader the next time it's attached, and the annotations will go with them.
If you're wondering why he unchecked the box, it's pretty simple. The app took too long to sync with his Sony Reader (he took a lot of notes.). He thought (and I would have thought) that unchecking the box wouldn't do anything beyond not syncing the notes.
That was the last straw. Without a reasonably intuitive and easy to use back up system for one’s notes and highlighted passages, I don’t see how the Sony Reader can be reliable for anyone who is reading with any purpose slightly more serious than beach reading.
I reluctantly sold the Reader through Craigslist and picked up a Kindle. The Kindle feels plasticky and cheap, and I have yet to get comfortable pushing buttons to turn pages. The thumb-dot-keyboard is awkward and feels superfluous after the touchscreen keyboard I was getting used to. But in the end, the Kindle backs up my notes wirelessly and keeps my books in sync between the Kindle, my laptop, and my iPhone.
He's not the only one to have trouble with Sony's PC app. When i got my hands on the new Sony Readers last fall, I tried using the app just to see how well it worked. The experience was so painful that I must have blocked it out of my memory. But I did find my notes from that period: "I loath the Sony Reader Library. Every time I use it I have to resist the urge to hit something." I'm pretty sure that's not an exaggeration.
P.S. There's an alternative to Sony's app which provides much of the same functions and is much less user-unfriendly: calibre. I've talked about this open-source ebook library tool before, so i won't repeat myself here.