If reservations are being made and upgraded two different ways, they must be maintained in two seperate records. The agent can "Link" the reservations together, but this is in reality nothing more than putting in a notification in each reservation that they are traveling with a party in a separate reservation. (With all the automation used to handle upgrades and rebooking seats when an different aircraft is used, that link doesn't do a whole lot)

Nothing I present is in any way sanctioned or authorized by AMRCorp.