If you’ve created an invoice with the Invoicing tool and matched it to a transaction, then the transaction will automatically move to ‘completed’, with the invoice attached as well as the VAT amount from the invoice.
If you’ve paid a bill through the ‘Bills to Pay’ feature, then the transaction will automatically move to ‘completed’, with the bill attached and the VAT amount you entered when setting up the bill.
All transactions, including those you have manually added from other bank accounts, feed into the VAT and Tax tools. The VAT calculation and sole trader tax estimation are based on the information you provide on transactions either through the transaction home page or in the Bookkeeping feature in Online Banking As such, you should ensure that the category, VAT amount and allowable tax percentages are correct.