Depends on what kind of transducer your talking about. If it is a trolling motor transducer then the only thing that matters is that it is pointing "down" into the water (sorry couldn't resist)
If your talking about a stern mount td and your rigging it to work on your t/m then I usually try and orient it like it was on the transom. But that is just how I do it.
Concur with above. The stern mount transducers I've used (Lowrance & Humminbird) on my trolling motors have a pointy end, which is mounted pointing forward.
I have very little experience with them, but thats mainly what I have used them for also. I am now learning how tell the difference in the type of bottom and to see baitfish and other structure.