Question: Is there an easy way to differentiate which information has been prefilled from the ATO and which has been uploaded from the QuickBooks file?
Its main advantage is to save time, reduce manual data entry, and improve the accuracy of tax return preparation.
Answer:
See below prefill view from QuickBooks

From ATO
“Prefill for ATO” is a feature that allows tax agents or tax practitioners to retrieve information already reported to the Australian Taxation Office (ATO) and populate the relevant fields in a taxpayer's income tax return. Learn more

Note:
There is NO prefill button for CTR and TRT, unlike for ITR which has that capability.
