Certified payroll reporting mandates require the submission of "weekly" certified payroll reports (if you read the fine print of the rules & regulations). Therefore, to accurately generate these weekly reports, you should issue your payroll on a weekly basis, as QuickBooks only recognizes payroll when the paychecks are cut, and not when the payroll is earned.
Certified Payroll Solution will handle bi-weekly payroll, however, it will report the full amount of the bi-weekly paycheck on the final certified payroll report. In "most" cases, adding a statement in the "Remarks" section on the Statement of Compliance "that payroll is issued on a bi-weekly basis and the amounts reflected on the certified payroll report are the total of that full bi-weekly check", will suffice.
However, we make no guarantees that this will be accepted by the entity that you have to submit the reports to.
When you issue your payroll on a bi-weekly basis, you will need to generate two certified payroll reports - one for each week of the pay period; in order to obtain the correct number of hours worked each day for each week.