Darren is correct. The AA timetable lists the flown mileage as:
(miles from Origin to Connection City) + (miles from Connection City to Destination
However you only receive AAdvantage miles for the point to point Origin to Destination.
In addition, if you book a 1 stopper now for anything in June or July there is an almost 100 percent chance when it comes time to fly the flight will no longer be direct. If you go to the gate the agent will print both boarding passes and attach the ticket to the second boarding pass. If you go to the ticket counter the agent will simply re-issue the 1 flight coupon. In either case it will still only count as 1 NA flight segment.
The main draw back to direct flights is that if you need to do a re-issue for a flight prior to that 1 stopper and that direct flight no longer exists you will need to re-do you NA segments to come in at 6 or under.
rich