For a room only reservation, payment is due at check-in. If you plan to pay at check-in, do not enter a credit card in the system for online check-in. It will automatically charge that card on the morning of check-in. I know that unless I call to pay the balance ahead of time, my card is usually charged by 8 am on my check-in day once I do online check-in.
I forgot once I wanted to pay by GC and when I got there, I decided to leave it on my card and just use the gift card for spending and a future trip. Some people have had them reverse the charges to the card and put it on their gift card, but I do not know how quickly the charges reversed on the card or how long it took.