If you filed your extension through your TurboTax software, what you paid with the extension should already be accounted for when you completed your return. How you can check this is by looking at your return. If you paid an amount with your extension on your federal return, this should show up on line 71 of Schedule 5. If it's there, then your additional balance due should be anything on top of your extension amount. If it's not on this line, then you can stop payment your extension payment check.
