What software are you using to run payroll? If you’re using the payroll site, they can export it straight to quickfile.
If you’re doing it with another piece of software, you should tag the bank payment to salary payment (it’s an option when you click ‘Tag Me!’). You should then create a journal to assign the payment to the correct nominal code (e.g. NIC etc).
Edit
Take a look at @Joe’s post for a guide on journals