Yes, you have to ask for YVR-MEL. As flychrisfly mentioned, the system will do the rest.
But just because you can see availability for YVR-HKG and HKG-MEL, doesn't mean CX will release Award inventory for YVR-MEL. So when doing the dummy booking, look for YVR-MEL because looking for two sectors with availability and trying to add them won't be allowed with CX when transiting HKG.
Other options may include looking for YVR to SYD, BNE, CNS, or ADL then adding a QF flight through to MEL. You'd have enough miles and sectors to do this.
Depending on your timeframes, you could also skip HKG early in you trip and go CDG-NRT and do the HKG stop on the way home.
Thanks for the explanation, I didn't know CX do married segments as well.
Unfortunately I had to stopover in HKG, it was to break my trip into two as I will do the MEL-DXB-LHR-CDG-HKG first, take a 6 months break and continue on with the HKG-NRT-YVR-HKG-MEL trip, just need to buy a cheap MEL-HKG revenue fare to break a big trip into 2.