I recently purchased a round trip ticket from LGA-MIA, which was significantly cheaper if purchased from US Airways, even though it was operated by American Airlines.

So, I booked it on US, and then I had to call AA to select a better seat without paying more money.

I couldn't do the upgrade request ahead of time, so I only got put on the upgrade list when I checked in at the airport.

I'm not sure if anything has changed with the upgrades, since this flight was before they merged the frequent flyer accounts. They may have sorted this out already.