Currently, there isn't a way to track more than one class per employee during a pay period.
As a workaround, you'll have to create a journal entry to tag Employee Wage to a different class, then offset the JE each pay run. Please consult your accountant first before doing this process to ensure you're doing an accurate record based on the type of business you have.
Here's how to create a JE in QBO:
Sign in to your QuickBooks account and go to the + New tab.