"Per IRS rules I think we can only contribute into company part of 401K if the business went in profit."
I don't think that that is correct. If you were self-employed you cannot make a retirement contribution without net profit, but you are not self-employed. You are an employee of the S corp and the S corp, not you, is making the employer contribution. Whether it is good business practice for a nonprofitable S corp to make an employer contribution (other than a matching contribution that might be required under the plan) is questionable, however.
Also who is "we" in the quoted sentence above? Your question seems to suggest that you are the only employee.
