Well sir, I struggled getting our gift certificate system working in a way I liked. (spoiler- We haven't launched our GC program because we can't customize the emails sent via online purchases. We're on SiteBuilder).
This problem was 1 of 3 major things that took a while to figure out. For this particular one, you have to edit/customize the form (and any other sales order/cash sale based form) to display "Gift Certificate" field in the item column listing.