As Jeff mentioned, you want the edge grain up for testing because this is the side that goes against the bow's window when shooting.
First, orient the flat grain run offs so that they run over your shelf/hand and then place the edge grain against the bow. As was mentioned, side against the bow is the proper side to spine. Having your shaft as straight as possible and using well seasoned shafts helps to elimate some of those deflection differences you're seeing. A little sanding of the stiffer sides can help even up the deflection if you have the weight to spare.
For very straight grained shafts that don't have flat grain run offs to any large degree you can can rotate your shaft on your tester to locate the stiff side. But as I mentioned, shaft has to be very straight for this procedure. Edge grain of a shaft isn't always the stronger side of a shaft. About half the time it falls on the flat grain. Or that's been my experience. When this happens make sure to orient this side to the hand/shelf.
ART B