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@bdk2 If you entered the payment made with the federal extension in the Deductions & Credits>Estimates and Other Taxes Paid>Other Income Taxes, the amount should have been entered on Schedule 3 and on the Form 1040.

 If for some reason you are not seeing the payment made on the Form 1040 Line 31 go to Forms mode and select and open the Tax Payments worksheet listed on the left of the Forms page.

On Line 9 of the worksheet, under Federal, enter the amount of payment made with the extension.  This will force the payment to Schedule 3 Line 10 and Line 15 which flows to Form 1040 Line 31.