Except for the purpose of a self-employed retirement contribution, you are not self-employed, you are employees of the S corp. The deduction for the retirement contributions goes on your S corp tax return, not on your personal tax return. The amount of your elective deferrals must be reported with code D in box 12 of the W-2s issued by the S corp.
The amount of your income that you can defer to the 401(k) is what remains of your W-2 box 1 income after subtracting any required income tax withholding, Social Security tax withholding and Medicare tax withholding.
