All I can tell you is that if you add any files to your Kindle, they will stay on that device but the books won't sync to other devices that have Kindle Apps. I worried about this when I added books to my iBooks app on my iPad and iPod but I have never been charged so my guess would be that you are safe. Keep an eye on the free sites like Kindle Daily Nation, Pixels and Ink, Books on the Knob and others. there are a lot of "iffy" books on those sites but occasionally a really good book shows up free for a time frame.
Have fun with your new toy!