From the TiW website:
Pre-Paid Reservations and Dinner Shows:
For any participating Walt Disney World® Resort restaurant where reservations are pre-paid, make sure to request the Tables in Wonderland discount at the time of booking for discount to be applied. A vailid Tables in Wonderland card must then be shown at time of ticket pick-up to retain the discount. A refund can also be given at ticket pick-up if the Tables in Wonderland discount was not applied at time of booking. Tables in Wonderland discounts for show times are subject to change without notice.
You will have to pay at the time you make the reservation. If you don't mention the TiW at that time, let your server know when you dine at CRT. They are used to refunding the TiW discount and will have no difficulty doing it at that time.