Use an agent for your permits. Commercial permits are lengthy and cumbersome. You’ll need to give 10-15 days notice. You’ll need an Operators Permit plus an Air Transport Permit.
There are CAA charges: Operators Permit: $500 Air Transport Permit: $250
If you are flying on any of the following routes M758, M646, M767, G334, M761, G580 ensure that you are not overflying any of the Indonesian islands. If so, you’ll need to make sure you also get an Indonesian permit.