If your voucher balance is less than the prepayment you want to make in the booking, you should make standard certificate redeem procedure when ordering, but after pressing Apply button the order page reloads. You stay on the order page, and the prepayment amount decreases to the balance of the gift voucher. The rest of the prepayment is paid with the other payment systems.
If the voucher balance exceeds the prepayment, after pressing Apply button you will see the warning about the writing off the total voucher balance for this order. If you press Continue, you agree with this condition. Then, you will be redirected on the order confirmation page. If you press Cancel, voucher won't be redeemed. You will have an opportunity to make a prepayment with the other methods.
Pay attention: you can redeem only one gift certificate on the order page.