Slotski My experience with city check-in was shortly before Codeshare started.
At that Time i used the QR desk for the 18.30 departure.
Until 15 Feb 2016 then the 1830 flight (CX645/QR5800) will check-in at the CX desk whilst the 00.01 flight (QR815/CX9201) will check-in at the QR desk. Exactly as happens in Chep Lap Kok.
After 15 Feb 2016 then both flights will use the QR facilities.