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Do I have to issue separate payrolls in QuickBooks® for each job my employees work on?

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Absolutely not - that would be a huge waste of time and energy; besides "most" certified payroll reports require that you report gross pay on the specific job AND total gross pay for the week for each employee!

Enter all hours worked by each employee using the QuickBooks® Weekly Timesheet function; assigning the appropriate job, service item, payroll item, and hours worked each day.  This information from the timesheets will automatically be pulled into your paychecks when you create them.

In the Certified Payroll Solution program, you can specify if a certain job (s) is not subject to prevailing wage/certified payroll reporting. 

Certified Payroll Solution first looks at the timesheets from QuickBooks and whether or not you have indicated that the jobs need a certified payroll report; and then, it will do the rest of the work for you.