A sole owner of a S corporation has a 401(k). The salary he gives himself is $50,000.  He defers $18,000.  As such, his W2 taxable wages is $32,000.  However, he also matches himself 25% of his W2 of $12,500.  

On the 1120S, on line 8, do you put compensation as $50,000?  Or, do you put the net taxable amount of $32,000?   I figured you put $50,000, because a shareholder of a S-corporation shouldn't have higher or lower net business income based on if an employee deferred in a 401(k).  Meaning, if the employee was non-related, and the employee put into the 401(k), the owner of the corporation would be disadvantaged tax-wise (through higher business income) if line 8 reflected $32,000.

The $12,500 is reflected on line 17.