Neither one. If you are using TurboTax Business, I recommend you enter your Salary and the payroll tax via the step-by-step. Your salary of $50,000 salary goes on line 7 - Compensation of Officers. The taxes withheld from your pay is not an expense, but the payroll taxes that the business paid is an expense. This would include the employer's share of Social Security and Medicare, and federal and state unemployment tax. Those payroll taxes will show up on Line 12 of the 1120-S, but are entered on the Tax and Licenses Worksheet.
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