You have to keep track of an account for the Gift Certificate. As long as the GC's account has a balance, anything/everything purchased comes out of the account.
When someone orders from you, they will contact you and say they want to use their GC. You get the number from them, subtract their balance from the GC's account. If it isn't enough to pay the whole amount, you send them an invoice for the difference (the balance). If everything's covered (or after you're paid that balance), you just mark it as "paid" with eBay and ship it.
If you sell GCs, make sure that you give them an expiration date, usually 6 months or 12 months. That way they will eventually "time out" and any remaining pennies that might remain get absorbed - or encourage the use of the GC before it dies, increasing your sales.
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Uncle JoeSharing Rainbows, One shirt at a Time
eBay Hall of Fame
Uncle Joe
Sharing Rainbows, One Shirt at a Time
eBay Hall of Fame