Here's my two cents.
First, this may not be what you want, but it's fairly easy to stock an ipad/ibooks with epub files. You can either email them to the account owner's email account or put links to it on a web page and just access the files from a browser on the ipad.
An alternative to upload the kindle files to your Personal Documents feature so it appears in the Kindle app on the ipad. After you activate the app, the tablet will have an amazon.com email associated with it where you can email files. (Check the help on it on Amazon).
There's a very important caveat. In late 2013 when I dropped files to my Personal Documents so they can be synced on my ipad's kindle app, all the ebooks would render terribly. (I had an ipad 1). After I did some checking, I learned that there was a bug in the ipad Kindle app which caused this to happen---and the only way to resolve it was to sync via itunes to your laptop via usb. Yuck!
1 1/2 years have gone by and with later ipads and itunes, these issues may have been resolved. But the fact is that the Kindle app's native environment is in android, so you would expect there to be some translation problems for another operating system.
On the Kindle app for Android, when you sync to Amazon's Personal Documents, everything looks fine.
Also in Android, using the native "Play Books" app to sync ebook files works very well (I was impressed). You upload it into play books from your desktop (most of the time), and then it magically shows up on all devices sharing the same google account. Note that Play Books also renders PDFs well too.
So to summarize, in my experience, the two best syncing solutions are in Android, not ipad/ios, and I have a slight preference for Play Books.
Update: I just see that Google Play Books is available from the Apple app store. https://itunes.apple.com/us/app/google-play-books/id400989007?mt=8 Because it's porting from android, I wouldn't expect its rendering on ios to be as flawless as it is on android, but it's updated often, and it's very easy to upload files to Google from any web browser on a desktop so that it renders on your ipad. That is probably what you want. I just downloaded the app and checked how it rendered ebooks. Looks great to me!