Most of the calls I have seen over the years have had the "short reed" at the bottom, although I have also seen a few with the short reed on top. Honestly, I am not sure what the value of using short reeds on calls is. There are so many factors that influence the sound and tonal qualities in mouth calls that it is difficult for me to believe that placing a short reed in a call has any real impact.
That is not say that using multiple reeds and staggering their placement near the front of the call will not impact the sound. It will. The bottom line is that experimentation in building calls is the only real way to determine if the use of short reeds really is a factor in sound quality. Then again, you could probably make several calls using the same "formula" in terms of reed numbers, spacing, thicknesses, tension, and cuts, and end up with every call sounding a bit differently. That's just the way it is with mouth calls.