Did you already file the return with the wrong payment amount?
If you haven't filed yet,
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 on left (or Personal for H&B Desktop)
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