Hi Ajgale-gale, 

With regard to the company settings, the branch number is an identifier for a business entity i.e. for multiple employing entities. For tax purposes, each entity is reporting individually under a branch number.

It is best to confirm with ATO as well what the branch number is for your business entity if you have multiple employing entities / branches. 

If you have further questions about branch numbers, or if this doesn't address your query, please let us know.