I applied for my visa early on when I first received the paperwork, but then was asked to renew my passport as it only had 10 months validity. Unfortunately, I neglected to update my passport number with the Australian authorities and had the gate agents scrambling a little to correct the problem when boarding the a/c for ADL out of HKG. Turned out not to be a huge deal, but I certainly wouldn't recommend it! So, update passport first, if needed, and then apply for the visa would be my advice!
Cheers!