When you put a shaft on a spine tester the up side is the side the tester measures so if that side is stiffer than the other 3 sides place that against the bow. Don't worry about the second stiffest side, it rarely works out resting on the shelf. The side against the bow is the important side.
With dowel shafts you also have to consider the grain "flames" to determine the nock end. Once you have determined that then do your spine testing. With shoot shafts the butt end(bottom, bigger) is generally the point end because the grain is around the shaft eliminating and grain variation.