(EDIT: USBill posted his response while I was typing mine!)
Once you have the Kindle app on your iPad, you are essentially out of the iTunes universe and syncing to Itunes has nothing to do with syncing your books.
In order to get your books in sync with each other, both your computer and your iPad have to be connected to the Internet. If you are reading something on your computer, when you close the program, it sends this information to Amazon. When you start the Kindle app on your iPad, it will check with Amazon and take you to where you left off, but it will only do this if you are connected.
Clear as mud, eh?