They will. If you do not send in a payment with the return and they still have your return, they will use your refund to pay the bill. However, if they process your return before they receive the amended form, they may send the refund to you. If they do send you the refund, you can use that to pay the amount owed. You do not have to do anything, unless your refund will be less than the amount owed, then you will have to pay the difference.
