I see what you mean. QuickBooks Online comes with a variety of "Pay Type" options, that you can 'activate' for each individual employee on an as-needed basis. By following the steps I listed above, you'll be able to 'deactivate' certain pay types for certain employees.

Take a look at this screenshot displaying what will appear when you edit the pay types for your employee:

By un-checking the box next to these pay types, they'll no longer appear as an option when you run payroll. You're unable to remove these options from the program, you're only able to deactivate them by un-checking their boxes.

I hope that helps to clarify things. Let me know if I can shed any more light on this for you.