In an S Corp if two people own 40% each and one person owns 20% how do you determine each salary?

Employment (salary) and ownership are totally independent. Salary should be exactly what it would cost to hire a complete stranger to do the same job, and if any "owner' cannot perform as well as a stranger, there should be  a provision in a contract or shareholders agreement providing that the employee/owner can be fired, while still retaining an ownership interst.  If your salaries are identical to the percentage of stock ownership, the IRS may argue that a part of the salary is really a "disguised dividend" and dividends, unlike salary, are not tax deductions to the corporation.