I have changed the item code for the various taxes in Adagio Invoicing and the GST shows on the invoice as well as the HST, but unfortunately the customer set up overrides the item and the rates do not calculate or show properly.

We have the tax tables set up for the various jurisdictions, the problem is with the calculations being done by Adagio Invoices. If you have 2 items with GST only and 2 items with HST, only the HST will calculate and show on the invoice (if the customer/header section of the invoice is set as HST) vice versa if you change the invoice header to be GST.