If your tax payments were greater than your tax liabilities then your tax return should show a tax refund for the overpayment.
The overpayment doesn’t show on my tax returns. They show how much I actually owe. However, I mailed in my paper returns with printed emails stating the tax payment confirmations and amounts on April 15th (have confirmation IDs on the emails). The mails have been postmarked to Oct. 16 but I e-filed successfully on Oct. 15. Will IRS and Utah State Tax Commission check my payment confirmations and issue me the refunds after they approve my returns?
If you have proof of payment for both the federal and state taxes owed being paid on or before April 15, 2019 with the extension request, then even if the payment was not reported on either the federal or state tax returns, both the IRS and your state should subtract the tax payments from the taxes owed being reported on your tax returns.
On a federal tax return the federal extension payment will be shown on Form 1040 Line 17 and on Schedule 5 Line 71
If you failed to enter the extension payments plus any other payments made from 4/15 to the date you filed then you MUST WAIT for the feds/state to process your return if you have already filed it ... they should catch the error automatically and correct the return for you. If they do not you will need to amend the return(s) later.