I have two questions please 1) Where do I add our VAT number as this is appearing on our invoices as XXXX 2) How can I customise my invoices to fit a window envelope?

Hello accounts254, Welcome to the Community.

You enter the VAT number you would go to Taxes>edit VAT>edit settings>input VAT registration number. ( It will show as xxxx on print preview when in Custom form styles)  

To customise your invoice to fit a window: Cog>custom form styles>Design>Select "fit printed form with payslip in window envelope"