I am assuming this is for a room only reservation. On-line check in will allow you to put a credit card in your file for room charging privileges. I think you're not able to do that with a gift card. With gift cards, you can call in advance of arrival and have the CM apply the gcs to your account so that you're essentially prepaid. Otherwise, you'd have to stop by the desk to have the gcs applied to your reservation. That wouldn't have to be done at check-in, however. You can do it later. I like to do it early in the morning when there is no one waiting in line.
HTH!