There is not really a place to enter an early Form 1040 payment made prior to completing your return. Include both of your payments (Form 1040 and Form 4868) as a payment made with your extension, Form 4868.
Go to Deductions and Credits > Estimates and Other Taxes Paid > Other Income Taxes > Payments with Extension > Payment with 2024 Federal extension to enter the total amount that you paid.
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