I have mine on opposite sides of the tank as well and they kind of make a "L" with their direction.
But, I also don't know if there's a right or wrong answer to this. Some people want flow to their rocks to keep detrius off, some want flow behind their rocks to clear the matter that settles back there. Some, as ann411 said want the flow to break the water column for gas exchange.
I guess some of the direction needed will also depend on what corals, etc you'll be keeping as some require more flow than others and some require less flow than others.
You'll probably find yourself changing the direction quite often, here and there. I know I've changed the direction of mine more than once because of one reason or another.
As for sounding ignorant....not at all. That's what this site is for. Everytime someone asks a question, everyone learns something and we've all asked these questions at one point or anohter...and I'm still asking them! LOL!