Base on the mileage requirement, i suppose that you are redeeming for y. It shows on expertflyer that there are limited seats in y on those flights therefore your chance to get the waitlist cleared is less than 50% IMO.

It has been reported that CX will charge you one way for both flights and refund the difference to you after you have completed all flights. You may ask the agent. But as mentioned, you have to bear in mind that the chance of getting a seat for inbound is not that high.

One more thing you may want to consider is about married segment issue. While there may be HKG-YVR avilaiability CX may not release seat for mnl - hkg - yvr. I have come across such situation where i have confirmed the long haul and would like to add a TPE-HKG immediately before my HKG-LHR flght; the agent said all tpe hkg flights were "full" within that 24 hours while i am seeing them wide open for straight redemption. Therefore you may consider changing hkg on inbound to a stopover (and visit the city for one day or two) to avoid such problem.