I asked Jim, or Academy Director, and he had had this question before. Here is his answer, and one I would concur with.
I would use the FLO line over the Spine line. The FLO line is tested over the full length of the shaft but the spine line is based on the shorter distance of the butt end. Personally I do both of these tests with my clubs but I insert the shaft into the clubhead so that it is secure and will not move on the shaft and do a FLO test with the clubhead on the shaft to find the best alignment.