I'll be paying quarterly for first time. Safest option is 100% of 2016 tax (safe harbor). Interview asks for option 100% and then calculates (2016 tax)/4. If I deduct the tax paid from paycheck, it takes me off the 100% option otherwise I'll be overpaying by the paycheck amount.
Definitely reduce the total tax by the amount that you believe will be withheld from wages. TurboTax would account for this based on your 2016 return when choosing to pay estimated taxes for 2017.
You don't want to include in your estimated taxes any portion that you believe will be withheld through wages or other sources. The key is eliminate penalty but not to overpay your account so that you get to use your money.
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