You may find the guide below to be useful.
Basically you can tag the net payment to your employee as NET Staff Salaries Paid, there is a specific bank tagging option for this and the tax + NI payments choose the option “Tax payment to HMRC (e.g. VAT, PAYE or Corporation Tax)”.
Now you need to take the figures from your payroll software and enter a journal to break down the PAYE, SMP, NIC and any other components of your payroll. This is explained in the following guide.
http://community.quickfile.co.uk/t/how-do-i-enter-payroll-paye-journals-and-entries/53/4