There are a few factors at play here. Depending on the bank that has offered you the card there are different types of overdraft protection that may have been set up.
Typically, if they attempt to run the card with no money, if one of these is in play, you will be spared any overdraft fees by the transaction charging to a designated overdraft account, usually savings, or by the transaction failing due to insufficient funds.
If you know the transaction went through, and you know there were not enough funds in the account to cover the transactions, then you have a few options.
If you have overdraft protection that auto charges insufficient funds charges to a separate account, then you have nothing to worry about. If you do not, most banks offer a grace period where you have until the end of the day to zero out your account, that is to say pay the overdraft amount and bring your balance to at least $0.
If this is a charge that occurred in the past, and you have already been charged an overdraft fee, there may still be hope. I cannot speak for all banks, but I know that Chase Bank offers a once per year overdraft forgiveness, where they will get rid of the charges if you agree to bring the account out of the negative. There is a chance other banks will do the same if you call their customer service.