This is the correct sequence of events from the very begining and you can check to see if this is what you have done.
Tap the App Store icon
Search in the upper right corner for iBooks
Tap on the iBooks icon in the upper left corner under iPad Apps
Enter your password when prompted to begin the download
Exit the App Store and find the iBooks icon on your home page
Tap the iBooks icon to launch the app.
Enter the words iPad User Guide for iOS 4.3
Tap the iPad User Guide for iOS 4.3 icon in the upper left corner
Enter your password again is asked to do so
The book should begin to download. When it completes the download it will appear on the bookshelf in iBooks.
If you are not taken back to the bookshelf view after the book downloads, just tap library in the upper left corner and you should go back to the bookshelf view and see the book on the shelf.
(Your last post has me confused. The book should not be on the App Page - not sure what that is)
Tap on the book to open it and there should be a row of brown dots across the bottom of the opened book with a brown slider bar that you can slide back and forth to go directly to the page that you want to view. The page numbers and page content appear as you slide the bar. There is also a search area in the upper right corner that is very useful. The search area and the keyboard appear when you tap the magnifying glass in the upper right corner.
Type a keyword in the search field and a variety of choices may appear in a drop down list under the search field. Tap on one of those choices to be taken directly to that topic. The keyboard and the search field will now disappear. Repeat the process as needed.
I know you are using the iPad original - I am as well - but if you are running iOS 4.3.2 - which I am running - this book is more comprehensive for use than the 4.2 user manual pdf. You can always keep the 4.2 manual in iBooks anyway and you will have them both for reference.