First of all check if your 1040 was filed and accepted.
Did you go all the way through the File tab, through the 3 steps and hit the big orange Transmit Returns Now button?
You can check your efile status here
When you efile you get back 2 emails. The first email only confirms the transmission. The second email says if the IRS (or state) Accepted or Rejected your efile.
When you log into your account you should also see the status and if it was Accepted or Rejected, Started, Printed, Ready to Mail, etc. What does it say?
Then if it was accepted the IRS should catch you made an extension payment and add it in for you. If your return wasn't accepted then......
If your extension payment did not automatically show up on 1040 Schedule 3 line 10 which goes to 1040 line 18d you need to enter it. So make sure it's not already there before you enter it!
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