1) Enter the amount from Form W-2 Box 1 under Deductions >> Salaried and Wages in the "Officers (>2% owners)" box. W-2 Box 3 is the amount of wages used to calculate Social Security withholding.
2) The amount from Box 12(a) Code D should be entered under Deductions >> Retirement plan contributions. You may need to check the box for "Already contributed to a retirement plan for 20XX" in order to open the entry box. If the S-Corp also contributed to the pension plan, add that amount to the entry from W-2 Box 12.
3) Shareholder-Employee Compensation includes all compensation paid to officers of the corporation (owning >2% of stock). Generally, this reflects the amount from W-2 Box 1. This amount appears on Form 1120-S Line 7 and includes fringe benefits such as health insurance coverage, but not elective deferral plan contributions made by the corporation.
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