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....