When selling gift certificates, set "No Tax" to on. See Turning Sales Tax On and OFF . You just want to collect $50.00 for a $50.00 Gift Certificate. Do not mix Gift Certificates with other items on a single invoice.
When accepting Gift Certificates as Payment, take them just as though they were cash. There is a place to enter them in our daily Excel sheet so that you balance correctly.
Your Book Keeper needs to be informed either when you sell Gift Certificates or when you take them, so that you do not get charged twice for the transaction. Sales tax is normally charged when items are purchased and the certificates redeemed.