After you file

Can anyone help. Similar issue here.

1. I filed my 2024 with 2020 W2 (ouch). My refund was 11,508.00.
2. I amended my 2024 tax forms with TurboTax and now my refund is 8062.00. TurboTax incorrectly assumed I received the 11,508.00 refund so it asked me to send the difference of 3446.00 back to IRS.
3. After looking at the forms I realize my mistake. So now I am owed 8062.00+3446.00=11,508 from the IRS. How do I correct this mistake? Do I amend on TurboTax and manually edit the 1040x form? If yes, how do I manually edit the forms?