There is no connection between the online and desktop programs. If you filed an extension with TurboTax Online, the payment with the extension will not automatically be entered in the desktop program. You have to enter it yourself. The payment with the extension would appear on Schedule 3, line 10.
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 or Update button for payment with 2021 federal extension.
