Tango is right - it's really hard to get American to credit flights, sector by sector to different schemes.
I've had to insist that they issue boarding passes with the right numbers on, only for some locations/staff to be unable to do it. Quite often I've been told that if the number is changed it doesn't print on the boarding pass!
I had a nightmare last year - when an AA sector was credited to AA and not QF. AA were good about it and reversed it - but they told me that they'd never do it again for me!