Sales opening stock and closing stock entries are not to include VAT if you are VAT registered. If you are not VAT registered then you will have to incur the whole purchase expense in your business and cannot claim back the VAT element from HMRC. Nor can you charge VAT if not VAT registered.
VAT and NI are payable/repayable to/from HMRC and are not P&L items. These are balance sheet items.
Your query sounds as though you may require some professional help!
Edited at 12 Feb 2017 01:52 PM GMT