My sister had a similar experience with tickets from NYC to Prague. They were about $850 per person on Delta or Air France, but only about $400 on Expedia with an Air France code share number (exact same Delta plane in all cases - only one nonstop in each direction per day). She got a Delta locator number, an Air France locator number, and an Expedia locator number, so she was able to log into the Delta website to choose special meals and the Air France website to choose seats. Everything worked out fine, and with a family of four, the savings were substantial.
So, congratulations, and just keep all locator numbers (from Expedia and from American) handy, as you may need to get into different websites, or call different companies, for different things.