I can't lodge my employees with the ato. they don't come up on the list for lodging

Welcome to the Community, @kymleask. I can see the urgency to lodge your employees with the ATO. 

To make sure they come up on the list for lodging, I'd suggest you tick the box for Closely Held Employee. 

For more information, check out this help article: Create and lodge a pay event. It helps you learn about how to lodge pay run in QuickBooks. 

Let me know if you have additional questions, @kymleask. I'm always around here to help.