Typically, you should always use the ticket at least once prior to doing any upgrades. If the ticket was purchased at a discount (from a 3rd party reseller like undercover tourist), by using the ticket at least once Disney will credit you the current full gate price of the ticket when you upgrade. If you don't use the ticket first, Disney will only credit you what the reseller paid for the ticket.
Only tickets that are part of an upcoming room/ticket package can be modified before arrival. All other tickets can only be upgraded on-property at either a park ticket window or guest relations location.
You can upgrade them but you should use them first.... I did this with my tickets through AirMiles (Canada). We used them once to enter the gate then I went to Guest Services and upgraded them to our APs. Quick and easy peasy