Last year we had to go to guest services at the parks. But it definitely was not an hour long line. I guess it just depends when you get there. We were there no more than 10 minutes from ground line to leaving for the parks. We did it at the Studios side, maybe it’s less crowded?
Not sure about doing it at the resort but my friend upgraded hers on our way out of the parks one afternoon. I think the trick is to go to guest services ‘inside’ the park and don’t go at opening or closing. Took us about 10 minutes as well.
I stayed at PBH in June and was able to upgrade our tickets to Season Passes so I'm sure you'd be able to upgrade to a different annual pass. They seemed to be able to do most things that Guest Services could. Like @damo mentioned, you do this at the attraction desk located just past the lobby.