Except for the purpose of a self-employed health insurance deduction, you are not self-employed, you are an employee of your S-corp. Unless you have a SARSEP plan established before 1997, SEP contributions are employer contributions only. The contribution to your SEP IRA must be made by the S corp and is deductible on the S corp's tax return, not your individual tax return. The maximum your S corp can contribute to your SEP IRA is 25% of your W-2 compensation and is reported on the W-2 box 12 so you don't enter it again in the program.
