When you check in. You have the option of an alternative payment method other than what you used to make your reservation. For example, when youo check in you can pay the balance in Disney Gift Cards, cash, different credit/debit card, etc
I just looked at my CC statement from our last 2 trips. Both times, the room balances posted to my statement on our check-in date. Anything we charged to the room posted the day we checked out.