Submitting All Pay Runs to ATO through Gov Connect for the first time

I have only two Casual employees who are employed intermittently and I have yet to submit a pay run to ATO through Gov Connect. I tried to submit the last pay for the Quarter through STP Payroll on Reckon One. The YTD figure came up for only aone employee on that pay run as the other employee didn't work that week. My question is: Do I have to submit all pay runs for the July - September Quarter individually? Is there a better way?