Hey khardu,
The VRN number will automatically show in the invoice header when entered in the Taxes settings. In the UAE version, the box to enter this number will be the 'Business ID No.' It will then show on the invoice against the Tax Agency name, e.g. HMRC Agency Registration No: XXX.
You can create multiple agencies with custom tax codes on the taxes centre in QuickBooks by going to Taxes > Add Tax > Custom Tax if you have not already created an agency for HMRC.
For the correct business ID/VRN no. to show on the invoice if you have multiple agencies, you will need to select a VAT code associated with that agency on the invoice under 'TAX'.
Please let me know if you have any further queries :)