Yes, pay only the balance you owe on the amendment after subtracting your original payment of tax due. You can try the following to enter the tax paid, it would seem the payment with your original return should come into the return, however you may be able to add it by using the steps below.
- Deductions and Credits > Estimates and Other Taxes Paid > Other Income Taxes Paid in 2021 > Income Taxes Paid
- Scroll to Other Income Taxes Paid in 2021 > Withholding not already entered on a W-2 or 1099 Revisit/Update
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