MEL-PER-DPS is two seperate flights (& flight numbers) and so the upgrades would be seperately treated if they were able to be done on both sectors.

The good news means you will only have to fork out for the MEL-PER cost of an upgrade, if available.

The aircraft that flies up to DPS from PER has business seats (738 I think) though it is sold all economy. Not sure what the chances of bagging a more comfortable seat, but others will advise the approach here, though it would depend most likely on the status of the passenger.

There is a way around the reservation problem, but I am not an expert, best I leave it for others to reply who understand these airlines reservation systems.