I made an estimated prepayment with the extension I filed, but that amount is not being deducted from the amount I owe?

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 Taxes (or Personal for desktop H&B version)

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

A payment with an extension is not the same as an estimated tax payment. They go in different places on your tax return. Make sure you enter the payment as a "Payment with 2023 federal extension." It should appear on Schedule 3 line 10 in your tax return.