Fuel that is NOT used to propel the vehicle (like reefer and APU fuel) does not apply to IFTA. You should always fuel reefer tanks or APU’s separately so that you have a positive record of those gallons/liters NOT mixed in with those going into your propulsion tank.
The Federal IRS code allows for you to claim fuel tax that is used in BUSINESS USE but not in the propulsion portion of the vehicle to be refunded back to you via Form 4136. The full instruction containing this exemption can be found –> HERE
If you do not have a separate tank for your reefer or APU, then there is language in the government’s document (link in the previous paragraph here) which provides that you if can accurately separate the truck gallons from the reefer or APU gallons via other means, then you can still apply for a refund via Form 4136.
And don’t forget to check with your state filing jurisdiction tax authority also. It is likely that your state has a tax refund for their fuel tax on non-propulsion fuel too!
However, for IFTA purposes you want to only enter “propulsion” fuel into your IFTA calculations. Just make sure to keep your receipts and documentation straight in case of audit!