Do you have a power user subscription?
If so, if you go to Account Settings > Design Customisation, select ‘Advanced customisation’ and click ‘Global Scripts’, drop this line of code into the box, save and activate and job done! 
(check out the topic linked below for better instructions)
$(".chkVatIncInvoicing").attr("checked", true);
http://community.quickfile.co.uk/t/run-custom-scripts-within-your-quickfile-account/9126