Thanks for the additional information.
If you are adding directly from the bank feed, it sounds like the transactions have previously had a purchases VAT code assigned prior to accepting into QuickBooks Online and the system is remembering this when you are adding the transactions now and therefore pulling to the VAT 100.
To record VAT payments correctly, you will need to do this from the Taxes tab and record the payment/refund against the filed return. Once recorded here, you would simply match the VAT payment recorded with the transaction as it appears in the For Review tab in the Banking screen without a VAT code. To give you help with this, please refer to our online article with reference to section 11 - Recording you VAT Payment.
In regards to the payroll expenses, check to see what VAT code has been used on the transaction by clicking into it and changing to the appropriate VAT code or No VAT as needed.
Let me know if you have any queries. Or, if you'd like to go through this over the phone, you can call our dedicated team who will be happy to assist you. Our contact details can be found here along with our opening hours.