Client missed recording payroll chq and has already filed payroll taxes for the period. If we record this properly in QBO how will this affect the payroll tax reports?

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Record the missed Payroll cheque with the correct dates. To capture the Payroll taxes from the missed payroll cheque: When you file your payroll taxes next month, be sure to set the date parameters to not only the previous month, but the month that the missed cheque was recorded to. For instance: the missed cheque was a March cheque. When you pay your April Payroll Taxes, select the period from March 1 to April 30.