Same issue here, and as far as I can tell, this isn’t possible. I’ve not seen a gift certificate system for woo yet that actually treats gift certificates as an actual currency, instead of some ‘discount’ to be applied before everything else is calculated.
We have this problem on a client site using the gift-certificate-pro plugin from ignitewoo – they just create ‘coupons’ in the general system, but coupons are applied before the checkout page. A true ‘gift certificate’ system would have the option of using the gift certificate as another form of payment.
I keep wanting to think this is ‘in there’ somehow, but I’m about 95% sure this just isn’t possible.
