Currently yes, the amount is automatically deducted at checkout; but I think ideally (and this is how our old system ran) you could "choose" to pay with your gift certificate just as you would choose PayPal or Credit card, etc.

Even more ideally, I think, would be a text field for a code, which would then free up the "users to certificates" relationship. Maybe that's not an ideal situation, but I can see why some shops would not want to restrict it to users who exist in a database (like a free promotion period where a bunch of certificates are printed and distributed to potential customers).

Haven't seen TCS on here in a while and I'm not sure what his plans are for this module. (Or if something like it is being considered for inclusion in Core?)