Roughly when OLCI opens, tha airline takes over travel agent tickets so that part shouldn't make a difference at the airport. However, look at your receipt carefully to check whether you have a published fare or some sort of bulk or consolidator fare from AmEx. That could create problems too.

If the ticket was purchased within 24 hours, you should be able to call AmEx and cancel for free, then purchase a new ticket with the AA flight number at prevailing fares for the AA marketed version of the flight. It could be cheaper or more expensive, but chances are that AmEx ticketed it under the codeshare to save money.

BTW, have you checked IAP fares for premium economy and business class? If you have a fairly expensive coach ticket, there's the chance that a discounted premium cabin ticket could be cheaper.