Though I fly Sky-hero Spy (Y6 configuration), it is relevant to the 3DR Y6:

Initially I connected the 6 motors as suggested in the APM Copter instructions. The copter was unstable, throttle reaction was very sensitive and yaw was terrible.

I then changed the rotation direction of the rear motors (i.e. 4 and 6) and switched between connectors 4 and 6 in the APM input. So now tall 3 top motors rotate clockwise and all 3 bottom motors rotate counter-clockwise.

It now flies like a charm !!!!

BTW - I use APM 2.6 with external magnetometer