Fuel purchases made while operating under a fuel trip permit should be included in total gallons purchased to calculate the miles per gallon and in the tax-paid gallons purchased (if taxes were paid at the time the fuel was purchased) for the appropriate jurisdictions.
You must include the miles traveled while using the fuel trip permit in total IFTA miles. It should be a part of the total IFA miles travelled in the jurisdiction, not as taxable miles travelled for that jurisdiction.