If your extension payment did not automatically show up on your 1040 or state return you need to enter it. So make sure it's not already there before you enter it! Federal Extension payments should be on scheduled 3 line 10. And go to 1040 line 31.
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