Hi daniald,
Using classes is a great way to track employees and payroll accounts in QuickBooks. QuickBooks Desktop Payroll makes it simple to save you both time and effort while putting everything into the correct accounts automatically. I can explain how the class system works with QuickBooks Desktop Payroll.
When applying a class to an employee, you can do so simply by going into Employee center>Edit Employee>Payroll Info. However, at this time you can assign one class per payroll run. To make sure everything is entered into the correct account I'd suggest talking to your accountant on how it should be entered. If you don't have an accountant we can help with that. You can go to our find an accountant page to find one in your area.
Our developers are always looking to hear feedback from what businesses are looking for. If you want to be able to add multiple classes per payroll run, you can submit ideas online by going to Help>Send Feedback Online>Product Suggestions.
Hope this helps.