How far away from arrival date are you?
If you are more than a week out, most likely the resort hasn't even seen your reservation to start the room assignment process. So I would just call and have whatever you wanted for your request to be added to the reservation.
If you are less than a week out, you can always change the room upon arrival if it's not what you want. It takes a little time, and kind of cancels out the time savings of doing the online check in, but you won't be stuck in a room you don't like so long as they have something you like better available. I have only changed a room one time at the front desk after doing online check in, and it took about 15 minutes longer than the standard online check in process.