Xero is the best bookkeeping software out there but you still need to know how to correctly code the GST component of each transaction. We use Receipt Bank for bills and receipts. When compliance falls due, we'll run a review of your transactions to ensure consistent and accurate GST has been captured.
Pay As You Go - this is the tax that you withhold from your employees when you pay their wages. These funds are sent to the ATO each BAS or IAS cycle.
Most likely you'll "lodge the BAS" every quarter. Depending on your business, you may have to lodge every month.