The Canadian tax system can be seen as complex and we get many questions on whether AutoEntry can handle them. Essentially AutoEntry doesn't actually do anything with the various GST/PST taxes as the various accounting packages handle them so well already, it means we don't have to.
With an invoice where there are one or more taxes, AutoEntry simply extracts the total tax figure from the invoice/bill. You then select the appropriate tax code as normal.
When the invoice is published through to your accounts package, it then splits out the tax automatically to the correct rates.