Yes, any estimated tax payments entered into TurboTax will be used to calculate your federal and state refund or balance due by TurboTax. Although the estimated tax liability may have been determined in the prior year, actual payments must be added to TurboTax to assure accuracy.
Estimated tax payment questions are asked toward the end of the TurboTax Interview.
To add your federal, state or local estimated taxes paid for the current filing period:
Select: Federal>Deductions & Credits> Estimates and Other Taxes Paid>Estimated Tax Payments and press "Start" (or "Revisit").
Your state or local estimated tax payments will be automatically transferred from your federal worksheet to your state return.