The charges are only for sending personal documents (say, a Word document or PDF) through Amazon, having them convert it, and even then, you're only charged if its sent back to your Kindle via 3G. If you use Wifi that service is free (and in my limited experience, very awesome).
The syncing of book location between Kindle and iphone or other devices is free as well. But I think that only works for things you buy from Amazon. I don't think "sideloaded" via USB cable will sync. I'm not sure about things Amazon converts for you.