In general, you have to pay in 100% of the tax liability of the previous year or 90% of the liability for the current year on a timely basis to avoid a penalty for late payment of tax. As a practical matter, the IRS will calculate the penalty based on what they show in their records. So, the payment you make through TurboTax is only an estimate. If you owe less than that, the IRS will refund you any extra that you paid with the return. I can't tell from what you said if you owe a penalty, but the IRS will determine that based on the amounts you paid in and when they were paid.
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