Deductions & credits

Well ... either you made contributions  via the W-2 or not ... if you put the contributions in the non W-2 section then they are deducted on the form 1040 as an adjustment to income.   If you had made the contribution as your own employer then it would have been on the W-2 ... and if you are an employee of the S-corp then you should have done this thru the W-2 payroll system.