This is a very annoying feature of the way through flights work. I have had luck in the past going to the domestic gate and asking to be put on the upgrade list. One time they just did it, one time the GA had to get a supervisor who did it, and one time I asked before departing MAN if I could get an upgrade on the domestic leg and they did it before I got to ATL. I avoid the hassle now by not booking through flights, but that makes for a much longer day sometimes.