You can redeem an iTunes gift card onto your account : http://support.apple.com/kb/HT1574
Your account's balance can be used to buy content from the ibookstore, as well as iTunes, app store and Mac App Store. As long as your balance covers the full purchase price then only that will be charged, if it doesn't cover it then any remainder will be charged to your credit card on your account.
How purchases are billed : http://support.apple.com/kb/HT5582
When making purchases, content credits are used first, followed by Gift Certificate, iTunes Card, or Allowance Account credits; your credit card or PayPal account is then charged for any remaining balance.