When booking onboard, if you don't designate a
travel agent at the time of booking (transferring the booking to a TA after you get home), the OBC that you might receive from the TA is generally less than if you designate them at the time of booking.
But, I believe you can do that. By designating the same TA at the time of the onboard booking, they may be able to "work their magic" in getting you into the same room you picked for the original booking.