How can I deal with Setting up of a employee payment run (including super, wage and accounting for payg, payw) inclusive of any notification i have to do to the ATO

Manage customers and income

Hi cslawrence, this webpage has a bunch of helpful tips, and some getting started guides attached also. https://quickbooks.intuit.com/au/resources/product-updates/tips-setting-payroll-quickbooks-online/

Here is a STP specific guide also: https://support.yourpayroll.com.au/hc/en-au/articles/360000304455-Single-Touch-Payroll-STP-Guide

Hope this helps!