Sorry man, forgot about this yesterday....
I checked "the reef aquarium 3". It does discuss nipple orientation, but not as extensively as I had thought.
First they refer to some work by Richard Harkker. They described this work as being rather inconclusive as Harkker found that nipple orientation did have some impact on color and intensity, but therer were too many factors to come up with a universal answer.
Delbeek/sprung then said that in their exp it was a bit more consistent and they suggested going with the nipple up.
I guess in summary, they said try it up, but if the color or intensity seems off, try reversing it and see what you see.
They did also say that there has been a good amount written about it, so I assume that there are some other good sources/aritcles floating around somewhere....