Why do you insist on booking both sectors on the Qantas website? What advantages does that give you - besides printing a nice little "QF" codeshare number on your Jetstar boarding pass?
Even if you book both legs on QF as QF612 and QF5830 you will still need to collect your checked luggage at BNE and proceed to JQ check-in area for your PPP flight. That will not change.
Regarding what you said here; "Furthermore, I can book the whole journey on Qantas website, but it seems a direct booking is more expensive, so I decided to book seperately. In addition, booking directly can enable myself to select my favourite seat and may choose JetLight."
I take it you mean if you book the two sectors separately then it would be less expensive, ie. booking MEL-BNE on QF site and booking BNE-PPP on JQ site? Doing it this way you'll have the option during the booking process of selecting your seat on JQ and paying $30 for that exit row seat.
But you said booking "directly" will enable you to do this?
I thought your defintion of booking directly was booking both legs on the QF site, therefore I don't think you'd get the seat selector option for your JQ flight would you?
And also why would you be choosing the JetSaver Light fare if you just mentioned you'll have checked luggage to transfer between flights in BNE?