Once you get past the first click or two, you should find that adding ebooks to your Kindle app on your iPad or iPad Mini is basically identical to the process you used for adding it in the pre-iTunes 11 world. In fact, the process I'll outline for adding new .mobi books to your Kindle app is the same that you could use to add presentations to Keynote for the iPad, documents for Pages for the iPad, spreadsheets for Numbers, etc.

The basic problem is that the iPad and every other iOS device hides its file system from us. There's no "folder" or "file" so you can't tap on an ebook icon to open it up and read it, you can't tap on a photograph to open it up in the photo viewer, etc. The file system's there, of course, but it's buried under the iOS user interface. Apps that need to access the file system for individual items have to use their own approach (which is why the Kindle magically shows them while in Keynote you have to go to the "My Presentations" area in the app).

Where this gets complicated is that Apple doesn't want us to get to the file system in iTunes either, so the capability is rather tucked away in an unlikely spot in the iTunes app, and that's only accessible when you have the device hooked up.

Let's start by grabbing the fun classic novel Ivanhoe from FreeKindleBooks.org. You can grab a copy too: Download 'Ivanhoe' for the Kindle.

Now plug in your iPad Mini (you could use wifi sync, but let's go all old school for this demo!) and find it in iTunes 11. In case you've still not quite mastered that, on the top right you should see a button that lets you get to your devices:

Click on it -- you can see I have 3 devices -- and find the iPad Mini:

Click on the Mini and you'll see the usual summary view. There's a new set of tabs that shows up too, along the top:

What you want is in the "Apps" area, so click on that and scroll to the bottom of that page. I think few people realize that there's anything below the app management window, actually, but there is!

What you're seeing above is a list of all apps on the iPad Mini that have permission to access the file system and what documents they have available. For me, it's just the Kindle app.

Click on the Kindle icon and the right side changes:

Almost done. Now click on "Add..." on the lower portion of that window and select the ".mobi" file you've just downloaded:

That's looking good, there's now the new book (albeit with an unfriendly name) listed:

At this point, simply "sync" your iPad Mini with your computer and after a few seconds the new book will have transferred onto the device.

On the Mini, tap on the Kindle app to start it up and don't panic if you don't see the book appear immediately! What you need to do is tap on "All Items" at the top since the .mobi books aren't considered Books, per se, just documents. Once you do that, the new ebook appears on the lower right:

Tap on it, perhaps rotate your device, and you're ready to read of the adventures of Sir Ivanhoe!

If you're working with other iPad apps that have files the process is very similar in iTunes 11. And, if you've worked with previous versions of iTunes on this sort of process, you can see how it's really pretty darn similar, just that first step or two have changed.

Good luck to you!