If you have not entered a VAT settlement account within your system accounts as shown below, when you run your VAT Return and click Mark as reported you will see a note that this has not been setup and the transfer of amounts from your input and out vat will not be automatically generated.

This is not mandatory but it does save you time, your vat return can still be sent to HMRC and all of the transactions will be flagged as reconciled within your return.