QFSupport’s reply shows the mechanics of how you enter the appropriate journals, this post of mine attempts to explain why it works the way it does:
http://community.quickfile.co.uk/t/payroll-posting-issues/5999/4?u=ian_roberts
It sounds like in your case the employer’s NI (item 1 in my list) is zero, but the principle is the same. Employee’s NI does not show separately on your P&L, it is part of the “gross wages” amount.