USNA may not decide to which MOC to charge you until late in the process -- or they may have already tentatively decided but it could change. The charging process is a complex one that is only indirectly related to your appointment.
I agree that sending a thank-you to both would be an excellent move, if for no other reason that both thought highly enough of you to give you a nom. Congratulations on your appointment!
(And there is no way for you to know to whom you were charged until you're at USNA -- in our day at least, it was on some form we received at some point in the process. You can see that it wasn't a huge deal b/c I don't even recall which source it was for me.)