Since requested to have your federal taxes owed debited from your checking account, the Form 1040-V is not needed so can be discarded.
On your amended tax return if you have taxes owed you include a check for the taxes owed with the mailed amended return. Or if you are e-filing the amended return you can use the IRS payment website to pay the taxes owed on the amended return - https://www.irs.gov/payments
Note - The Form 1040-V was only for the original tax return that was filed.
