Port for sensitivity, starboard for speed.
I believe if the sub you are using only has one towed array, it is on the starboard side by default. I once tried switching to port array on a Victoria/Upholder class, and I just got a weird waterfall display and strange noises.
edit: Note, what I said at the top there is only a guideline based on the 688i and Seawolf classes, I don't know it to be true of every platform.