using a flat rate discount will subtract the amount from the grand total.
To be 100% honest, Gift Certificates in eCart are not supported.
There are many more aspects to consider with Gift Certificates than just subtracting the certificate amount:
1) How to ensure that they can only be used once
2) Allow the unused amount to be used on the next purchase.
3) Don't process through the gateway id the gift certificate amount is greater than cart amount.
If you would like assistance creating a Gift Certificate system, you should sign up for a premier ticket where we can work with you in a one on one scenario.