If all you have paid on the room is the one night's deposit, they will simply apply the entire amount you have already paid to the reservation, thus lowering your balance due at check in.
If you have paid the entire balance for the room in advance and you were booked on a room only, they will hold the money until you check in and you can put the excess amount towards any room charges you make. If you make no room charges, the amount would be refunded to you upon departure.
If you have a package reservation through WDTC and have already paid in full, they will refund the overage the same way it was paid (to your credit card if paid by CC, by check if paid by check, etc).
As to your Disney Visa, you would lose credit for anything that is credited back to your card. They would not remove what is already posted but will make the adjustment when the current month's charges get credited.