In order to try to make sure the front desk doesn't check you out using your credit card on file, I let them know when I check in that I will be using a gift card as partial or complete payment for the room on check-out, and ask them to annotate that in my file.

That usually works, but on the few occasions where it didn't (where they did an anticipatory "express check-out" using the credit card on file), I've been able to get it reversed when I do check out in person. Your problem should arise only if you *don't* check out in person when you leave, but rather allow the "express checkout" to be done automatically (and since you have the gift card, you'd almost have to check out in person for it to be used).

There is one other solution -- apply the gift card before check-out. At some time during your stay, make a "partial payment" against the final bill using the gift card. This ensures the gift card is applied, but won't guarantee to pay the full bill since the final amount is not known for sure until you actually depart.

And as BKKLEE notes, you can use multiple gift cards on one invoice.