Only if flying Qantas

If not flying Qantas, then check in is with the operating carrier. e.g. Fly BA and it is BA where check in is performed ( and as a OW Emerald will be able to use business line ) and , iirc, the check in signs above the desks show both BA and QF numbers or fly JQ and JQ will handle check in

QF check in desks are for checking in for QF flights