If I filed for an extension in April and I now have taxes due, where was my payment in April applied?

When you requested your extension you were supposed to pay your estimated tax due.  Did you enter the payment you made into your tax return?  Go to Federal>Deductions and Credits>Estimates and Other Taxes Paid>Other Income Taxes 

The payment that you made with the extension should be on Schedule 3, line 10. If you filed the extension from within TurboTax, the amount of your payment should have been automatically entered in your tax return. If it's not there you have to enter it yourself.

To enter the payment you made with your extension, type "estimated tax payments" (without the quotes) in the Search box, then click the link that says "Jump to estimated tax payments." That takes you to the screen that says "Estimates and Other Income Taxes Paid." Scroll down a little to the second section, "Payments with Extension." Click the Start, Update, or Revisit button for payment with 2021 federal extension.