I *believe* POR royal rooms have a pretty good discount - I don't know what % but I've seen a few posts on here of people saying "oh we were in room (type) but we switched to the royal rooms for a bigger discount". I don't think there's much discount at all at AoA though. On Jan 3rd you should be able to go on the website and price out various room/resort combos and see which one comes out best, but you can also call and get a quote immediately (even without the disney visa). If you're not happy with the discount you get, you can ask the CM to play around with the different room types, similar resorts etc and see if something better comes up. My original resort choice had a next-to-nothing discount but when I called back and asked the CM to check a few other options, she found me a great discount at a similar resort and I saved a bunch. If you're determined to have the POR royal rooms though, all you can do is take whatever the discount works out to be.
They can apply the code to your current reservation, unless you're switching from room-only to a package or the other way around, in which case they'll book a new one then cancel your old one once it's gone through.
