Try adding the surcharge to your Tax table.

You will need to add a new Customer Status to Tax types. If this status applies to most of your customers, it should be type 0.

You will also need to add a new jurisdiction for the surcharge to your Tax Group. If you want the surcharge to have GST calculated on it, the surcharge should be the first jurisdiction on your Tax group. When you set the rates for the surcharge jurisdiction, make sure that you modify Item rates and Customer rates.

When you have an invoice that is an exception, you will modify the Tax type for the invoice on the Header page of the invoice.