When a VAT return is due we will send you a calculation by email including the amount you need to pay HMRC. You can pay this online via  https://www.tax.service.gov.uk/pay-online/vat

You'll need your VAT registration number, and the accounting period which is the final month and year of the period you are paying (usually 03 / 06 / 09 / 12 plus the year).