I am running my first pay run ever. Once I finalise the run. The salary payments and Super payments have to be made independently. Is that correct?

Hi sanjaya261, 

Thanks for posting. 

You can make automated super payments via the Reports > Super payments page, but first thing is, make sure your business is registered with Beam. When you are making a super payment through Beam, it can take some time between when you initiate the super payment batch and when the super funds will receive it then have the payment status updated in QuickBooks Online Payroll. This link will guide you on how to do Automated Super Payments with Beam. 

Salary payments deductions that are being paid manually or to a bank account, you will need to update the payment option to paid to a super fund. Click this article for more about Salary Sacrifice Super payments. 

Feel free to drop by the Community if you have any questions.