You can't transfer your own books to the Kindle app. From the Kindle FAQ:
Quote:
Periodicals such as newspapers, magazines, and blogs, and personal documents can only be delivered to and read on Kindle devices and cannot be viewed on Kindle for iPad/iPhone or other Kindle applications
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You
can convert your .PRC files to .epub, using a program such as Calibre, and then read them in iBooks, Stanza, or IBISReader on your iPad.