I think you have to collect checked luggage from JQ and then check in at QF in BNE, Arthur. Of course if you are travelling Jetlite this is not relevant.
As long as you are able to check in to JQ in BNE no less than 30 mins before your flight to Whitsundays (40 mins with checked baggage) , I don't think it makes any difference how you do the booking.
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Philip
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