No, you would buy the AP minus what you actually paid for the ticket you are upgrading. So you would pay whatever the additional the AP would have cost.
Save yourself some possible aggravation and just buy the AP if that is what you want.
At the most, anyway you go about it, you would maybe save yourself the smallest bit of money, but in the end, would it really be worth it to have to go thru the upgrade process?
I just get my AP from universal. Job done. It is just not worth it for me to save maybe $5.
Honestly, 10 min of my vacation time is worth more than $5 and that 10 min is assuming there is no line you have to wait in, the transation goes completely smoothly. And in most cases, you will not even save that $5.