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Yes, you can enter the state and fed tax manually. ezPaycheck payroll software is very flexible.

Please refer to this article
http://www.halfpricesoft.com/payroll-software/after-fact-payroll-checks.asp 

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 
Can I prepare a check with a self calculated state and federal tax witholding?

I mean if I want the deduction for state and fed income tax be a different than the program caluclated. I tried to change the figure manually but I can't.