If you need to change a tax return that is already filed, then you have to file a Form 1040X to amend the filing. Just include the additional extension payment on the appropriate line. The IRS will adjust and give you credit for the additional taxes paid. If you are mailing the returns, I would also include a copy of the check and the extension form for reference.
Please explain what you mean by "fix and re-file" before you try to do anything else. Why do you need to "re-fie?" Did you really file the tax return? Has it been fully processed? If all you did was get an extension for 2019 and pay the estimated tax due, you are not re-filing----you are ready to actually file the return for the first time---the terms you use to explain really matter here --- so we need to understand what all you have done,
If the return has never been e-filed or printed and mailed--ever--then there is nothing you are re-doing.
When you requested your extension you were supposed to pay your estimated tax due. Did you enter the payment you made into your tax return? Go to Federal>Deductions and Credits>Estimates and Other Taxes Paid>Other Income Taxes
In order to e-file your tax return--when all of your data is completely entered -- go through all of the steps in the FILE section to a big orange button that says "Transmit my returns now." Until you click that button, you have not filed.
Then watch your emails.
When you e-file your federal return you will receive two emails from TurboTax. The first one will say that your return was submitted. The second email will tell you if your federal return was accepted or rejected. If you e-filed a state return, there will be a third email to tell you if the state accepted or rejected your state return.
When all of your data is entered, if you are getting a tax refund it will be shown on line 20 of your Form 1040. If you owe more even though you made an estimated payment, then the amount you still owe will be on line 23. It cannot be both--you cannot owe and get a refund for the same tax return.
If you have federal tax due you can pay by mailing your payment with the 1040V voucher, (which has the address printed on it, having the payment taken out of a designated bank account, or you can pay directly on the IRS website.