The amount of estimated tax you pay will factor into your penalty for late payment of tax, but so will the timing of those payments. You need to pay your tax in evenly for each quarter if you are relying on your tax from the previous year to determine your estimates.
Also, you can work through the underpayment penalties section in TurboTax under Other Tax Situations if you want your penalty to be calculated based on the timing of your income stream and estimated payments during the year. That would be your best option to reduce the penalties you are facing.
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