What is the correct way to pay quarterly 100% of 2016 when part of the tax comes from a paycheck? if i deduct that amount i wouldn't be paying in 100% quarterly.

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.