The payment that you made with your tax return was for 2023. The 1040-ES vouchers are for 2024. One has nothing to do with the other.
The vouchers are TurboTax's calculation of how much estimated tax you should pay for 2024. They are not sent to the IRS, and you are not required to pay them. (You have already missed the due dates for the first two payments.) Having a $9,000 payment due on your tax return certainly suggests that you should be making quarterly estimated tax payments. You are paying penalties and interest because you paid all your tax when you filed your tax return instead of paying during the year. One way or another you should determine how much you should pay. If you estimate your total tax for this year, pay 3/4 of it by September 15, since you have already missed the April and June payments, and pay the rest by January 15. You can use the vouchers from TurboTax, cross out the amount and write in what you are actually paying, or you can download a blank Form 1040-ES from the IRS web site. Another option is to pay online directly from your bank account using Direct Pay on the IRS web site. If you use Direct Pay you don't need a voucher at all.
