There's a discussion on syncing in general in the FAQ here
http://www.kindleboards.com/index.php/topic,73465.msg1183688.html#msg1183688, and a discussion on using the Calibre ASIN facility to "spoof" it for non-Amazon books here
http://www.kindleboards.com/index.php/topic,68023.0.html.
Things have changed a little since those threads were written, though, with the arrival of the facility to store personal documents in the "cloud". When this facility arrived, some customers got this email in late October:
Dear Kindle Customer,
As a past user of the Kindle Personal Documents Service, we are pleased to let you know about some improvements:
• Your documents are now automatically archived in your Kindle library (you can control this from the Manage Your Kindle page at
www.amazon.co.uk/manageyourkindle )
• Archived documents can be re-downloaded from your archive to the all-new Kindle, as well as Kindle Keyboard (Kindle 3rd Generation--requires the latest software update v3.3 from
www.amazon.co.uk/kindlesoftwareupdates) – you will be able to find and download your documents from any of these devices that are registered to your account.
• Now (just as with Kindle books) Whispersync automatically synchronises your last page read, bookmarks and annotations for your documents (with the exception of PDFs) across devices.
We expect to extend these features to Kindle apps (such as Kindle for Android, Kindle for iPhone, Kindle for PC and Kindle for Mac) in the coming months.
You can control these new features from the Manage Your Kindle page at
www.amazon.co.uk/manageyourkindle where you can see a list of your archived documents, re-deliver documents to your Kindle, delete any document from archive, or even turn off archiving for your account.
Learn more about the Kindle Personal Documents Service from our help pages at
www.amazon.co.uk/kindlepersonaldocuments.
Thank you for choosing Kindle,
Amazon Kindle Support
The interesting line is
"We expect to extend these features to Kindle apps (such as Kindle for Android, Kindle for iPhone, Kindle for PC and Kindle for Mac) in the coming months."
There's no sign of this happening yet, but we're all hoping it will happen sometime soon. Once this happens there shouldn't be anything to do: until then, you'll have to use the Calibre fix.