Yes, you are correct. The Schedule H only calculates what payroll taxes are due (social security/medicare/unemployment/income tax withheld). You will need to enter your payments separately as estimated taxes paid.
Enter your payments in the "Deductions & Credits" section using the "Estimates and other taxes paid" topic. Start/Revisit the "Estimated Taxes" topic and enter the dates/amounts of the quarterly payments made by your payroll company on your behalf.
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