This is the answer given to one of the FAQ questions on the Disney site.
"If you have a vacation package, you can
pay off the balance online or call (407) 939-7675. Guests under 18 years of age must have parent or guardian permission to call. For your convenience, you are able to use the payment method stored in your online account
.
FYI; the onlince payment function has not worked in over a month
If you have a room-only reservation, you will pay off your balance when you arrive at your Disney Resort hotel."
Or you can call and make payments over the phone. We do this because we use discounted GCs and do not want our CC on file to be charged on check-in day.