I see you're an ExecPlat, so if you don't keep your AA number on the booking you won't get your upgrade. I'd wait until your upgrade is confirmed, then call in if you can't change the account online. You shouldn't lose your upgrade (though some airlines like AC insist on using their account if you are eligible for upgrading and you'll lose it if you credit the flight to any other airline program) but remember if you've still got onward segments or the return and those upgrades haven't been confirmed, change back to your AA number after you've flown the segment.