If you have the dining plan there is a place on the reservation page to link your resort res. and you won't be charged anything. You will still have to give cc info just in case you fail to cancel within the specified time frame and don't show. For CRT and the other dinner shows the penalty is the full amount. Most character meals and signatures will only charge a $10 no show fee per person.
Before you finalize the CRT res it will give a total amount that will be charged to your card. If it says it's the full prepay amount then it failed to link to your resort reservation. In that case it would be better to call the dining line and make the res over the phone.
I had a TIW discount that was credited to my card when I had dinner at CRT. I don't remember if I had to give the server my credit card, but I'm sure Disney has a protocol in place.
To the other poster regarding guaranteeing res with a gift card: I think I read that it has to be a credit/debit card because there's no way of knowing if you'll still have any money left on a gift card months later and thus no way to collect the no show fee if necessary.