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.  Note that PTO usage or any other device attached the vehicle that does not have its own motor separate from the propulsion motor counts toward IFTA and cannot be refunded.
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 at the end of the tax year when you file Income Taxes.  The full instruction containing this exemption can be found –> HERE
If you do NOT have a separate tank for your reefer, generator, 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 fuel usage from the auxiliary fuel usage via other means, then you can still apply for a refund via Form 4136 when you file your income taxes at the end of the year.  For example, if you know how many gallons per hour that your APU uses, you can do the math and apply for a refund for the fuel tax paid on fuel burned in your APU.
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!
When adding fuel manually into a return here on the site you can add auxiliary fuel in the auxiliary fuel box.  This can be ACTUAL amounts that you put into a SEPARATE tank, or they can be ESTIMATED amounts that you figure you have used in an auxiliary device like an APU, reefer, generator, etc.
YOU CAN GET YOUR AUXILIARY FUEL REPORT from the "Report" tab in the Switchboard HERE.