If you paid the tax (not the TurboTax fees) with an extension, the payment with the extension should be entered in your tax return. Then the tax return will show no payment due, and TurboTax will not ask you how you want to pay.
To enter a payment you made with an 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 2022 federal, state, or local extension, as appropriate.