If your extension payment did not automatically show up on 1040 you need to enter it. So make sure it's not already there before you enter it!
Federal Extension payments should be on schedule 3 line 10. And go to 1040 line 31.
You can type estimates paid in the search box at the top of your return and click Find and it will give you a link to Jump To the screen where you enter Extension Payments.
To enter the amount you paid with an extension (including state extension) go to
Federal Taxes (or Personal for desktop H&B version)
Deductions and Credits
Then scroll way down to Estimates and Other Taxes Paid
Other Income Taxes - Click the Start or Update button
Next page second section Payments with Extension
Either Visit All or Click Start or Update by the extension you paid
FOR A PENALTY ON LINE 38
You might be able to eliminate it or at least reduce it. You can go to Federal Taxes tab or Personal tab, under Other Tax Situations and select Start by the Underpayment Penalties. You will answer a series of questions that may reduce or eliminate the penalty. Or you can elect to have the IRS figure the penalty for you. It's form 2210.
It's under
Federal or Personal (for Home & Business Desktop)
Other Tax Situations
Additional Tax Payments
Underpayment Penalties - Click the Start or update button
