I've added discounts on two trips. The first time they just rebooked my package and I had to make new deposit, then they credited me back the original money. Seemed like a lot of work, but that's what they did. Most recently, I added the kids play/stay discount to my package, which I already had $200 down on, and all they did was apply the code. I just had to put $200 more on my Disney Visa to get it the discount. No new ressie. Either way, you should be able to work it out and get the savings.
PS- If you don't have to rebook, they will adjust your statement with the discount and email you a new one and your new balance showing any previous payments.