On the bookeeping column for banking it shows no VAT even though I will have entered invoices with VAT. Will this affect our VAT return?

Hello Wendyletheby, thanks for posting on this thread, So when you match the invoice to the transaction it will record it with whatever is on the invoice rather than the transaction, so if the invoice is say 20% but the transaction is no vat it will when matched record it as the 20% that's on the invoice for you because the payment doesn’t record the VAT anything initially declared will be on the invoice.