Hi tracynz, 

Thank you for your response. 

When you click on Download journal button on a pay run, an Excel file will be downloaded. Do you import this file then in QuickBooks Online? Please note that if a payroll journal is successfully exported to QuickBooks Online and you import the payroll journal manually it will cause duplicate entries. Download journal option will only show if the payroll journal is exported to QuickBooks. 

I would recommend to contact our Customer Support team to do screen share and to further check on the set up. 

Feel free to post again if you need any help with QuickBooks Online. Have a great day!