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yes that seems to be the general consensus here.  If that is the case, what is the penalty for filing Payroll at the end of December for Q1, Q2, Q3, Q4?  How does estimated quarterly payments factor into this if the s-corp officer has already paid all estimated taxes thinking he is self employed per the CPA's recommendation.

How do do Payroll when the State Labor and Withholding office states there is a 30-90 day delay in getting the state # to even file set up Payroll and with holding /unemployment. 

Can this be done in Jan or Feb retroactively?

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Again - seek professional help.  There are ways to mitigate/reduce some of the penalties.  Knowing that is what I get paid for.