Depends on your motor, if using a basic motor, for smaller dishes, one cable, from the LNB, goes into your motor, then from the motor to one of your tuners. This tuner is set to control your motor, in the tuner settings, the second cable goes directly from the LNB to the second tuner, on your receiver, this tuner is set up as second cable to motorized dish.
If using a larger, 36v, motor, which has 4 wires, going from the motor, to a V-Box II, then it's slightly different.
What type of motor are you using?