Change of amount owed due to payment

When I originally filed the 2019 taxes, we had an amount due to the IRS of $5807. We included information for the amount to be taken directly from our bank account.

On 5/27/20, 10 days after we electronically filed, we decided to make a partial payment toward our balance and went online to the IRS and paid $2,396.05.

We contacted the IRS and they have told us that Intuit/TurboTax will be the party that determines the withdrawal amount.

How can we get the amount to be paid changed from $5,807 to the balance of $3,410.95?

Do we do a revised filing? Or can we get someone to change the amount to the balance owed?