Can you clarify what you mean by iBooks app or in store?
the iBooks app uses an ePub format, so if you buy a digital book from somewhere else, and as long as it has no DRM, you should be able to drag the file into your iTunes (books section), transfer it to your iPad and it should open up in the iBooks app.
iBooks is the name of the ebook reader app from Apple. iBookstore is the in-store feature of the iBooks that allows you to buy books. If you want to import other ebooks (unprotected ePubs only), you can do so via iTunes. It has a books section for you to drop the books in.
its my understanding that you would have to buy it directly from the iPad, every book is essentially an in-app purchase. thats why the actually iBookstore app is not pre-loaded and needs to be downloaded from the App Store first.