In addition to emailing, there is a mini Amazon program/application (guess you'd call it that) where you can "Send to Kindle" from your PC or Mac. There is a check box in the pop-up you get and so you can choose to have the item added to your Archive.
I've used it successfully to send an e-book to my various devices and apps, then have had no trouble using other devices/apps to access the Archive and get that particular book. The Whispersync function works for this method. Note that the "Send to Kindle" doesn't only mean the actual Kindle; I've sent to my Kindle app on my iPhone. Then, later, after downloading it to my actual Kindle, again, the Whispersync is right there.
Just another way to get books back and forth - and have them 'sync-able."
Now I see there is also a "Send to Kindle" for Google Chrome and Mozilla Firefox browsers. Gonna have to check that out...