Upgrading on AA / Multiple Award Programmes
 

I'm used to doing online upgrades with BA, it would appear this isn't possible with AA. Can anyone confirm this? Do I have to wait until I check in and ask an agent?

Also, My itinerary involves AA and Cape Air. I'm using my BAEC for the AA flight, but would like to use my AAdvantage account for the Cape Air flight. Anyone know if I can split programmes over an itinerary? Thanks!

AA allows to request "500 mile" upgrades for domestic flights online. All other upgrade avenues (miles, miles&copay, SWUs - AA generally does not do cash upgrades) require a call.
In order for this to work, you need to have your AA number attached to the reservation as well.

Splitting programs between segments does work in theory - if you get the timing right: You will need to change the FF# between check-in and boarding the Cape Air flight. That may or may not work....

AA does not offer POUG's like BA, but may offer a cash upgrade at checkin, however you will only be credited with your underlying fare class so would not earn the upgraded avios/TP's.