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You can follow this guide to add a customized deduction for Roth 401K and withhold it from each payment automatically.
http://www.halfpricesoft...w-payroll-deduction.aspx 

Please feel free to contact us if you still have any questions.

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 
How to do set up employees who elect Roth 401k withholding?