I did exactly what you've suggested and entered the amount under "Payment with 2020 federal extension" and the amount does not show up on 1040 schedule 3 line 9. My taxes were essentially finished when I filed for my extension in May and the amount that I owed was paid at the time, nothing has changed (in retrospect I should have just filed then, but I wanted some extra time to review it). Any idea how to fix this?
