For STP Phase 2 the common pay categories, leave categories, and deduction categories in the system have been updated with Payment Classification information, so you don't need to update.
If you don't use the common categories in QuickBooks Online Payroll, you'll have to check the payment classification of your pay categories, leave categories, and deduction categories to ensure you're reporting each category correctly to the ATO.
Once you've checked the settings and payment classification for each category, you're all set for STP Phase 2 and can lodge your pay run and pay event in the same process in STP Phase 1.