Yes of course and you should....but you MUST run all Employee compensation through your payroll app. You cannot give Employees compensation outside of payroll.
The IRS requires ALL compensation that you pay to an Employee, so if you are handing out bonus checks, make sure you run them through payroll.
If you give Employees money outside of payroll you are evading taxes...that is how the IRS views it.
See also How do I pay myself?
See also How do payroll taxes work?
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