If your company is registered for VAT, you can reclaim the VAT element of any expenditure on fuel provided by your company for use with company cars. This usage includes both private and business mileage. In return, HM Revenue & Customs (HMRC) require a charge to be paid. This charge is calculated for each vehicle from the scale charge tables in HMRC Public Notice 700/64 Motoring Expenses. You can work out the charge using the HMRC website https://www.gov.uk/fuel-scale-charge

When you've calculated the scale charges for each company car, these should be posted within the Cashbook Receipts option:

As per screenshot above, enter a Contra/Adjustments account in the Cash A/C box and a zero value in the Total Amt.

On line 1 of your posting choose the Fuel Scale Charges Expense account and post the fuel scale charge amount followed by the standard rate VAT letter - i.e. 238.00S.  Pressing <Enter> will calculate the net and tax amounts from this.

On line 2 of your posting select again the Fuel Scale Charge expense account and then in the amount field enter the amount as per the charge, including VAT, on the first line but with a negative value.  Leave tax code blank or select a ‘Out of Scope’ VAT code.