When I upgraded, the CM who helped us was very nice, but not very experienced. It took an hour, and he forgot to give us our AP cards until I asked. When I asked about applying the cost of my Memory Maker as a credit toward the purchase of the APs, he said we couldn't do it. I knew that wasn't true, but I just let it go. When I got back to the room that night, I emailed guest services. The next day they contacted my to tell me that they had put a credit on my account for the amount I paid for the MM. It was really easy-- super customer service. I hadn't activated the MM, so the worst case scenario would be that it would sit in my account until I took a trip where I would want to use it, but it was nice to get the credit.
Two bits of advice: 1. Upgrade on your first day if possible, so you can use your AP discount for food and merchandise right away. 2. Know ahead of time what your upgrade should cost, because my CM told me the wrong price at first, and it was $300 too high. He figured it out eventually, but it helps to know what you're supposed to be paying.