The iBooks cannot by default run external displays for "spanning" at high resolutions than the built-in screen's 1024*768. Out of the box, it only supports "mirroring" of the built-in screen to the external screen.
However, there is a firmware hack that enables regular spanning. Although most users have had no problems with it for quite a while (it caused some problems for some when it was first released), it should be noted that it voids your warranty.
You can get information about the spanning hack by simply Googling for "ibook spanning hack" -- remember that Google is your friend.
That same hack enables "clamshell mode" (operating while closed) which also is not available out of the box on iBooks.