Can you set up 2 separate payroll's within your accounting system for example Company A has 10 employees and Company B has 5 employees. You would do 2 separate pay runs?

Hi Sue, 

So that I can better support you on this, may I clarify if you have 1 or 2 ABNs for the 2 companies, please?

If 2 companies are under 2 different ABNs, I would suggest getting an additional QBO file for the 2nd business and do the payroll from there. 

If 2 companies are sharing the same ABN, you can set up 2 locations in payroll and process payroll for the 2 locations separately. Here is an article on how to set it up:

• Locations

  • https://support.yourpayroll.com.au/hc/en-au/articles/200028229-Locations

Please take a look and let us know if you have any follow up questions on this. Thank you.