The Toolkit calculates your VAT to pay or reclaim based on your allowable tax amount.
For example, say you have a utility bill of £120, with VAT charged at 20% (£20). As you work from home, you only want to claim for half of this utility bill as a business expense. In the Bookkeeping section, you would set the allowable tax amount to £60 (i.e. half of the transaction amount), the VAT rate to 20% (as per the VAT charged on the bill) and this would automatically calculate the VAT for your tax return as £10 (i.e. half of the VAT charged on the utility bill). This is so that only the business portion of your expense is recorded for tax and VAT purposes.
Please note that situations where the claimable VAT amount is higher than the allowable tax amount (e.g. costs of dealing with an HMRC enquiry) are not currently supported by the Toolkit.