Officially the difference is from the price you paid. However, I and many others on this board have upgraded LMT tickets and just had to pay the difference from full price, not what I paid. I have seen reports that some other third party tickets they can "tell" what you actually paid for the ticket but that either doesn't seem to be the case with LMT or many of us have received pixie dust on this.
I guess the bottom line is plan on the difference from the price you paid and hopefully you'll be pleasantly surprised and it will be the full price difference instead.