How do I get back to the first page of an application when I'm in the middle of it?

It really depends on the application. In iBooks if you tap at the very top of the screen, it will bring up the navigation buttons, including one that says "Library". That will take you back to the main screen of the application.

The shelves should show the ibooks that you've got in the app i.e. your downloaded purchases from the iBookstore. At the top of the shelves there should also be a Store button (for browsing, purchasing, re-downloading books from the iBookstore), and Collections (where any PDFs that you've synced/copied into the app go).

There is a chapter on the iBooks app in the manual, which can be downloaded from here http://support.apple.com/manuals/#ipad

Usually you tap the button that is at the top-left of the screen. In iBooks, this is labelled "Library" which takes you back to the Library of all your books.

If you actually want to go back to the first page of the specific book you are reading, tap the screen and you'll see a row of book pages along the bottom. Tap the first one.

In iBooks you should have a line of dots across the bottom of the page (assuming that it's an iBook), with a box around one of the dots - drag that box to the left-hand end to go back to the start of the book, or to any other position that you'd like to go to in the book. PDFs in iBooks show mini pages at the bottom, but it's the same principle - one page is highlighted which you can then drag.

Other apps will probably have a different way of doing it.

No, you will need to read them in the Kindle app. Most ebooks have digital rights management on them, so you can generally only read them in the store's own app - so iBooks for iBookstore purchases, Kindle for Amazon ebooks etc.

Sorry, misunderstood. Meg gave the answer, tap the page and you should get a line of options at the top of the screen, on the left-end of which is Library