I am Currently using Quickbooks 2012 and use the HMRC Basic Tools for the payroll and have got rather confused with the entries. I have been using the write cheque function for about 2 with Gross Salary and then individual deductions, but last November the employment allowance was only part of the Employer NI owed and now I cannot seem to get it to balance in the chart of accounts. What would be the correct way to record the payroll each month? Have been looking at this problem so long now I cannot see the wood for the trees
I havent entered payroll into Quickbooks so no idea how to do the technical processing bit. But the journals are the same regardless. When you actually pay the staff - process it through the net wages - that might be where you are going wrong. Heres a little something I created when I first started to help me get my head round it. Hope it helps.
Best thing to remember is that the net wages account should always revert to nil when youve paid everyone (unless you are perhaps running more than one payroll). I suggest you prepare everything you need to key before you start (excel or even just on a big bit of paper) and then back up your data before you start to key anything and do regular backups as you go along then if you get stuck you can unravel it easily.
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Joanne
Winner of Bookkeeper of the Year 2015, 2016 & 2017
Thoughts are my own/not to be regarded as official advice,which should be sought from a suitably qualified Accountant.
You should check out answers with reference to the legal position
What would be the correct way to record the payroll each month? Have been looking at this problem so long now I cannot see the wood for the trees 
