Tax Accounts for eBTax for Canada

 After creating the taxes for Canada GST, HST, PST our accountants decided they wanted to use differents accounts for each tax--I created the tax accounts at the Tax level. After reading documentation it indicated that autoinvoice uses tax rate tax accounts. Since I have already set the accounts at the tax level, eBTax will not allow me to do so at the tax rate level.  Would autoaccounting use the accounts at the tax level?  if not what should I do to correct the problem?