I had a similar issue. I emailed to ask if they could take the certificate out of the price, but because I have credit card in place already , it was billed straight through and I received no response. I would offer the suggestion to the moderator that they also have a setting for those that receive certificates to be able to pre-set that we want to use them. This way when one wins a bid, LL knows to subtract the certificate before charging one's card.
Perhaps others can also offer other easy methods to avoid chasing down LL for their very generous VIP certificates?