I'm no instructor but if you get on edge the current will push you down river. If you are trying to go perpendicular to the current staying flat will help you stay on top of the water and will minimize the drag on your hull.
Try both ways a few times on the same ferry/current and you should notice the difference. It all depends on where you want to end up and how fast you want to get there.
Same is true for leaving eddies, I used to carve out of eddies on edge every time and haul 4$$, now I stay flat and it seems to be more gentle than having to lean over to counteract the water grabbing my edge.