Basically, I don't think Quickbboks desktop is working at all correctly for Qualified Overtime. 

Here is an example.  An employee has 1 hour of overtime. She is regularly paid $20 per hour. Her overtime of time and 1/2 would be 30 for that hour.  If I enter 40 hours at $20 per hour, and 1 hour at $30 per hour, then her time and pay are calculated correctly, however, I believe she should not be paying SS and Medicare taxes on that $10, and we should not be paying matching on that $10, but we are.  The Qualified OT tracks as a company paid item, but it does not affect those payroll taxes at all, it is just tracking it. So I believe we will be overpaying our company matching taxes, and the employee with be overpaying her deductions. 

I then tried to set it up with 2 payroll items. One extra hour at the regular wage of $20, and then 1 hour at the 1/2 time wage of $10.  However this had the net effect of calculating her as actually working 42 hours that week which is incorrect, and then makes her vacation and sick hours accrue incorrectly, and also it still did not calculate the payroll taxes correctly. 

So I believe this is a bug in their system and they need to fix the payroll tax withholding capabilities of Qualified OT. 

I guess we will find out when we go to file our 941's?!