Yeah, I'm confused, too. Basically, a transducer shoots straight out from itself. If the transducer is mounted at an angle, then it will measure at an angle. So, generally, you want it pointing straight down. Otherwise you have to use your high-school trigonometry to figure out the true depth based on the displayed depth (and of course, that's assuming the depth directly under your boat is the same as off to the side where the transducer is measuring).
Now, on a sailboat, whenever it is heeling, you still have to do a little bit of trigonometry to figure out the depth. So I suppose that the ideal situation would be to have two transducers, each aimed at your "normal" angle of heel, off each side of the hull. Then you could see the actual depth whenever you were heeled. Of course, if you're that obsessive about it, then you would also want a third transducer pointing straight down, for when you are motoring and such.
In any case a transducer measure straight where it is pointing, and you have to take that into consideration when you are using it.