You can apply external forces to the vehicle's rigidbody with Rigidbody.AddForce() or Rigidbody.AddForceAtPosition() from FixedUpdate().
In Vehicle Physics Pro, you can access the vehicle's rigidbody from an add-on component like this:
public override void FixedUpdateVehicle () { vehicle.cachedRigidbody.AddForce(myCustomForce); }