Estimated tax payments are entered by the user of the software totally separate from taxes withheld on a W-2 or Form 1099. For tax year 2019 estimated tax payments are on Schedule 3 Part II Line 8. The total from Schedule 3 Part II Line 14 flows to Form 1040 Line 18d. The Form 1040 Lines 17 and 18e are added together with the result entered on Line 19 as your Total Payments.
There is and was no other way to enter the estimated tax payments.
Contact the IRS since the error is on their part as you should never have received your estimated taxes back as a refund from the IRS. There should be a phone number on the letter you received for payment due. The IRS should waive the penalty and interest since it was their error and not yours.
