No. In terms of WaveWall protecting you from radiation, it does not make any difference which way you put your phone into the case. As long as the WaveWall case is placed in your pocket the right way round (see this question), it will intercept the radiation your phone produces.
However, when thinking about the best way to protect your phone against damage, we recommend placing the phone screen against the flat side of the case. This will ensure that your WaveWall Classic provides the optimum physical protection for your phone.