I don't think the orientation of your S3A's will change the bass response noticeably. The wavelengths of bass frequencies are much much larger than the speaker. If you had a height mode issue it is slightly possible that you could place the LF woofer in a null. You will probably want to keep the tweeter near or at ear height so overall I don't think there is much to explore in that avenue.
I do recommend that you experiment with the distance from the front wall, and your mix position. Your software will help you find the optimum spots.
DD
Sound Sound - Homepage