duducting from the grand total instead of the subtotal only really makes sense in the case of a percentage based coupon.
If it's a flat rate coupon, the discount will still be the same whether it's taken from the subtotal or grand total.
if you are asking about percentage based discounts, you really cant take if from the grand total which is calulated as:
(subtotal + shipping + tax) - discounts
to do this, you would need to edit the WA_Cart_Coupons_PHP.php file. the line that calculates the percentage will look like:
you would need to edit anywhere that is appying the pervcentage discount to include shipping and tax, for example:
$appliedCoupon[sizeof($appliedCoupon)-1][1] = round($cart->TotalColumn("TotalPrice")*($nextCoupon->Amount/100),2);
would become:
$appliedCoupon[sizeof($appliedCoupon)-1][1] = round(($cart->TotalColumn("TotalPrice") + $cart->GetTax() + $cart->GetShipping())*($nextCoupon->Amount/100),2);