Every system can handle different FF program for the segements across a stopover, the info from GB is that only Sabre can handle it for a transit. AA uses Sabre, QF/BA use Amadeus. So book the reservation using AA RTW desk (which is the best way to book in any case) and have them enter your choice of FF number for each sector. Then you are all set and nothing to do at the gate (as long as you don't change your mind).