Thank you SH. I have decided to book flights seperately YVR- SFO/LAX on AC website and SFO/LAX - AKL on NZ website, it is almost the same fare but this way I'll be sure to have everything in order and I get the best of both worlds .
On the AC website fare class "L" is listed for the codeshare which should earn miles however on the NZ website "L" booking class doesn't. I know different airlines have different booking classes, just don't want to have any surprises after such a long trip.