Your taxpayer isn't going to include Estimate Tax payments as a business deduction or expense. Those are personal payments.

As you work through their tax form, you get to the point where you see the amount of Taxes owed. Then there is a section for various credits to be applied against the amount owed. That includes any prepayments that were made, whether that is from Estimate or Withholding. These are Prepayments. They are not Taxes.

That gets you to the part where the taxpayer either has a Refund owed to them, or a Balance they owe to the IRS.

You might want to review any places you maybe did this incorrectly.

As an Employer, your taxpayer should have had Payroll activity for that employee, which would include Fed and State such as FUTA is Federal Unemployment (employer-paid only), but SUTA or SUI (State) can be a mix. It depends on that taxpayer's State. You should get with a payroll mentor to review how payroll flowed for that taxpayer's business entity, to confirm it is correct and to help you know what is Business expense and what is not (gross payroll vs net). You mention W2. What about W3, 940, 941/944, State reporting?