You will have to select the taxes option > set up VAT enter the details, first month you would like to start tracking VAT, whether you would like to use cash or accrual, whether you use FRS, entering the relevant percentage, enter what periods you would like to file your VAT and enter your VAT registration number. Then when you create transactions with a VAT code the transactions will be populated within the VAT/Taxes section and it will calulate the amount due to HMRC.
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