Use file vat or run vat summary Vat 100 report and use the file vat button there.
This then posts the journal and payment to the Vat vendor or supplier account normally HMRC and if a refund HMRC - Receivable. in Customers.
Do it to paper and pay later if its first time so you can monitor the route posted.
You do need to set up he Vat supplier account as the Vat agency first to see this use manage vat option.
To pay off select pay bills in the pay bills section select the Vat agency supplier account and simply set the credits if available against the bills.