If you are using the WooCommerce EU VAT Number plugin and want to display the customer's EU VAT number on the invoice, you can insert the following macro in any of the 4 custom blocks or the footer of the invoice:
{{_vat_number}}
Similarly, to display any other custom field input on the invoice, simply insert the custom field's key in the same way, e.g. {{my_custom_field_key}}.