Under the Flat Rate (Cash) Scheme, you don’t have to set the VAT amount for each outgoing transaction. For income transactions, you charge the appropriate rate of VAT for that supply on your invoice. Then the VAT you pay to HMRC will be calculated based on the gross transaction amount (inclusive of VAT) and the flat rate you have set in your VAT settings. This will automatically be applied to your income transactions and will feed through into the VAT tool. 

For expenses, you can’t reclaim VAT, (unless you mark the transaction as a recoverable capital good). As such, in the bookkeeping feature, you are not prompted to add VAT information to move the transaction to ‘completed’. 

You only need to assign a business category and upload a receipt or an invoice to move the transaction to ‘completed’.