If you are running payroll in your business, you’ll need to do this through payroll software that can submit your “RTI” (Real-Time Information) submissions to HMRC. 

If you are managing your own accounts yourself, then you might do this using accounting software.

If you have an accountant, then they will most likely use a payroll bureau where they run the payroll for many clients in one go.
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Coconut doesn’t offer any payroll services, so if you have specific questions about your tax affairs, you should speak to an accountant or tax advisor.