You don't pre-pay at any of the Signature restaurants except CRT. You have to include a credit card number on all reservations for the $10 per person no show fee that will be assessed if you don't cancel the reservation within the required time frame and then no one shows up for the reservation.
Without the dining plan you will have to pre-pay the entire amount for the dinner shows (Hoop De Doo, Spirit of Aloha Luau and Mickey's Backyard Barbecue) and CRT. If you add the dining plan later you can either call and arrange a refund or wait and get a refund when you pick up the tickets for the dinner shows or at the restaurant for CRT when you dine.
If you use a gift card to pre-pay, be sure to keep the gift card because the refund will be returned to the card you used.