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Yes, you can enter the state and federal taxes manually. You can refer to this article for step by step guide

How to enter federal tax and state tax manually
http://www.halfpricesoft.com/payroll-software/after-fact-payroll-checks.asp 

Please let us know if you still have any questions.

Thank you.
Casey
Please feel free to contact us directly  if you need assistance
Small Business Payroll & Tax Software Solution
https://www.halfpricesoft.com 
How do I/can I override the calculated taxes on an employee paycheck? (ezPaycheck payroll software) I want to enter the federal and state tax myself.

Thank you.

Mike