If you leave your credit card number on file and use your room key to charge things to your room account, your room account would begin with a credit (whatever money you are due because of a discount you got after paying full-price for your room.) The credit would apply towards any charges you make.
You won't automatically get the discount if one is offered. You will have to call Disney and ask them if they can apply the promo to your reservation. Once that is done, if the trip is already paid off then they will credit the credit card that you used to pay it off. If your trip is not yet paid in full, the balanced owed will just decrease.
Room only discounts are when you reserve just a room and not a package with MYW tickets. If you book a package and a room only discount later comes out, I'm not sure that you can convert it to a RO discount. Generally when you have a room reservation with a deposit, and a package discount is later announced, you can't convert it to the package. Disney would refund your deposit and rebook the reservation.
