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
just to be sure about procedure...i swap signal wires wich goes to APM of motor 4 and 6 and change rotation of them?