You cannot amend an extension form. All that form does is give you extra time to file your documents. It does not give you extra time to pay. The estimated tax due has to be paid by July 15, 2020. Just pay the correct amount by whatever means you plan to use, and enter the amount you paid into your tax return so that when you file the return the amount is credited to your final amount due (if any).
Go to Federal>Deductions and Credits>Estimates and Other Taxes Paid>Other Income Taxes to enter the estimated tax you pay.
You have until October 15, 2020 to e-file your actual Form 1040 if you have an extension.