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Enter the payment on your tax return. You get credit for it on your tax return.
If your extension payment did not automatically show up on 1040 Schedule 3 line 10 which goes to 1040 line 18d you need to enter it. So make sure it's not already there before you enter it!
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
When you file your actual tax return, you list the amount that you paid as an estimated payment. That may be why the amount you owe now is much less than you expected. If you have already filed your return and you did not list the estimated payment that you made, the IRS will eventually catch up and send you a refund or your overpayment, although it may take a while.
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