I think you need to have a standard rate on Products and the ability to vary Sales Tax on Invoicing.

There should be a Sales Tax file to be selected during the Invoice process, I don't know about the Canadian system but it is a good idea to include the Sales Tax code down on each Invoice line. The Sales Tax value should also be stored on each Invoice line item.

When rates change if you store the standard Sales Tax Value you will need to reprice however wholesale Price changes often follow Sales Tax variations.

Simon