I have several nonprofits as clients, and the fact that QBO Payroll does not allow to assign more than one class per employee is the reason why it is not a suitable system for many organizations.  Not being able to "open" the paychecks and break down wages into several classes (very common in organizations with multiple grants to report) is a deal breaker.  I have also sent several requests to Intuit, but so far I have not seen any changes.