In the past, you were not able to upgrade tickets purchased as part of a package. That may have changed with the new "Magic Your Way" ticket structure.
I would advise you to post the "upgrade tickets from a package" question on the Theme Parks board and hope that Golden Oldie replies. If you are allowed to upgrade, you will get the DVC discount (provided you can show you qualify).
Since you are allowed to upgrade package MYW tickets, I'm very sure you can get the DVC discount on the AP or PAP pass when you do.
Best wishes -
P.S. GoldenOldie posted this in another thread:
Prior to 1/2/05, any ticket that was part of a WDW package could not be changed at all including upgrading.
With the advent of the MYW tickets and packages this has changed. You can now modify package tickets including upgrading and adding options at Guest Relations as well as at your resort front desk. The only thing you still cannot do is upgrade a package ticket to an AP/PAP/SP at a resort.
So you have to go to Guest Relations at one of the parks or in DD if you want to upgrade to an AP or PAP.