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Yes, you can enter different city tax rates for each employee .

You can follow this guide and add a new deduction "City tax". You can specify the tax rate from employee set up.

How to add a new payroll deduction and withhold it from each paycheck automatically
http://www.halfpricesoft...w-payroll-deduction.aspx 

Please feel free to contact us if you still have any questions.
If you have further questions, please contact us directly at services@halfpricesoft.com
Small business payroll & tax software solution
http://www.halfpricesoft.com 
Posted: 2017-09-22T13:50:39Z
Is it possible to enter additional local tax rates for paychecks
Posted: 2017-09-21T18:51:40Z