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Yes, ezPaycheck can work for trucking company. You can use the MISC check feature to write a check for the non-taxable reimbursement easily. Please try it.

Here are some links you may like to read too.

Trucking Payroll Software: How to Create a Paycheck by Mileage
http://www.halfpricesoft.com/payroll-software/create-paycheck-by-mileage-rate.asp 

Trucking Payroll Software: How to Create a Paycheck by Load
http://www.halfpricesoft.com/payroll-software/create-paycheck-by-truck-load.asp 

Please let us know if you still have any questions.

Thanks,
Casey
Please feel free to contact us directly  if you need assistance
Small Business Payroll & Tax Software Solution
https://www.halfpricesoft.com 
I have a truck driving company and we have perdims that are non taxable. Can ezPaycheck handle it?

Thanks,

Sweeney