I would personally have to say that the goniometer is virtually useless in this situation. Possibly more effective means of measuing lumbar flexion is using a standardized position, and have the individual bring their arms down parallel to a wall (standardized for subsequent measures), and use a tape measure to measure how far off the ground the tip of their hands are. Additionally, if this is not possible use a string along the persons back and measure the change in movement observed from specific spinous processes.
However, if you choose to use the goniometer, best bet is to find the ASIS, follow one edge down along the femur, and use the other as the free edge.