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Since the new payroll system doesn't have an option to add the employee's payroll ID. It would be best to contact their support to further assist you with this one. You'll want also to try other options recommended by Intuit Zac when changing payroll systems during the financial year. 

In QuickBooks Onlne, if the company uses QuickBooks Payroll powered by KeyPay to lodge pay events to the ATO under Single Touch Payroll (STP), you will have to lodge a Finalisation Event to send the final year-to-date figures to the ATO. To start this process. juyts follot the steps below:

1. Go to the Employees tab.
2. Select the Reports section (between Approved Leave and Payroll Settings).
3. Select Single Touch Payroll under the ATO Reporting column.
4. Click Create Update Event.
5. From the drop-down menus, select the financial year and pay schedule.

If employees have been paid on multiple pay schedules throughout the financial year, just complete the finalisation event for the pay schedule the employee is assigned to. Before you lodge the Finalisation Event:

1. Navigate to the Update Event created above. To access it from the STP page, click on the number in the ID column.
2. Confirm payroll data by clicking on the Actions button, then Excel. You can reconcile this report with other payroll reports such as the Detailed Activity Report to ensure figures match.
3. Resolve Errors in the Warnings tab.
4. Enter Reportable Fringe Benefit Amounts (if applicable), by clicking on the pencil icon in the RFBA column next to each employee.
5. Mark employees as ‘is final’, by ticking the ‘Is Final’ box for each employee. This is  to indicate to ATO that the employees have no further payments to be made in the financial year. It will also update the employee’s income statement to ‘Tax Ready’ so they can lodge their tax return.
6. Request Client Authority if you are lodging as a Tax/BAS agent.

Then, lodge the Finalisation Event by clicking on Lodge with ATO. If you need further assistance about this one, please contact our Payroll Support Team. They'll pull up your account in a secure environment and help you with this one. Feel free to visit our Payroll page for more insights about managing your payroll in QBO.

I'd like to know how you get on after trying the steps or after contacting our support, as I want to ensure this is resolved for you. Just reply to this post and I'll get back to you. Take care always.