Hi Lauren You will always only see month and year in config. When you click on the next tab PAYG Instalment, you will see to report by month or quarter. Also you will see Cash or Accrual. Put the Dot on which is your reporting basis.
So if you are doing a Quarterly BAS, in Config you choose October 2016. For monthly BAS December 2016 but you will have to make sure you have put the dot on Monthly.