Dealing with alien beings
The aquatic scenario works - maybe a situation where food is plentiful above the surface but with lots of predators below. Lots of creatures have work-arounds, like the spy-hopping of orcas or the nictitating membranes of some crocodilians or the antics of Archer Fish,, but I don't know of any vertical eyes. Turning things around isn't impossible.
But the interactions might be much more of a problem - as you say, humans have a hard enough time understanding each other. Where would we be if the aliens thought more like, say, cats, or dolphins, or giant squids? Women? :)