I have a room only, staying in August. I have paid the entire balance due with gift cards, by calling in. Each time I have paid with a series of cards, get a confirming email with balance due (now, nothing), and a suggestion to save the cards in case there is a problem. I was also told each time i applied cards that it might not work, but it always did (knock on wood).
I did not do online check in because I had not yet paid off the balance. On online check in, you have to enter a credit card number for incidentals. I wanted to do online check in after I paid, but I really don't want it to charge my credit card by accident. I am so paranoid after all the reports about Disney's computer systems.