Just hook them up in the way that seems right to you, it won't hurt the board even if they are backwards. In fact, the only connectors that matter which way they are hooked up are the HDD LED and the power LED. And they are easy to test, because they won't come on if they are backwards.
BTW, that is a great case. I got one from newegg as well, and it dropped my temps a lot. I will never buy another case that isn't Enlight!