If you have a side finder unit, you will want the xducer facing the same direction as you face so that your left and rifght don't get mixed up. If you don't have a side finder type, the orientation should not matter since the transducer transmits a circular cone, and there is no determination of left or right inside that cone that can be translated to the one dimensional display. The most important thing will be finding a way to keep the xducer level and not tilted one direction or another.
I'm about to have to find a way to mount a transducer on my kickboat. I'd be interested in hearing how other folks have rigged up their xducers too. I'm really interested in finding a way to mount it where it won't get beat to hell. Under the seat seems like the most likely position, but I'm certainly open to other suggestions from other folks who have already done their's.