Actually, I don't believe an onboard-booking for a future cruise is charged directly to your current onboard account. They will ask if you want to use the same credit card as the onboard account, but it shows up as a separate transaction, not listed in the onboard account charges. If you really want to use the gift cards for the future booking, I wouldn't apply it to the onboard account unless instructed to do so. You may need to visit the Future Bookings desk in-person with the gift cards, rather than simply returning the card to the box.
Enjoy your cruise!