I don't know if the changeover to the new system impacts your situation (i.e. if you bought the ticket prior to the changeover, the system may not be able to do it), but this is generally very easy -- one of the better features of the site. I just did it yesterday, in fact.
You just call up the reservation by the confirmation code. Then, you click on "Change Reservation," which is one of the options in the list on the upper right-hand portion of the page. You enter your new reservation details, choose your flights and when you get to the payment page, it has applied the value to your new ticket for you.