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Yes, you can use the MISC check feature.

How to Handle Housing Allowance
https://www.halfpricesof...ll-housing-allowance.asp 

You can also use MISC check to pay reimbursement to employees, such as the reimbursement checks for mileage, food, phone and other costs.

Thank you,
If you have further questions, please contact us directly at services@halfpricesoft.com
Small business payroll & tax software solution
http://www.halfpricesoft.com 
Hello,

Is there a way to enter nontaxable housing allowances separately from taxable payments?

Kindest regards,

Janet