There are different fields for entering frequent flyer number. When you redeem miles for your flights, the account the miles are coming out of is FQTR, but there are other fields (FQTV, etc.) that can be used to add your other frequent flyer numbers.
I usually find CX agents to be friendly, but being Gold myself there could be a bias. I just redeemed a ticket for a friend who has CX account but opted to have AS number included in the reservation, and I just CX agent asked for that, straightforward.