Whats the most efficient way to switch between 2 open windows on OSX ? (OR What am I doing wrong ?)
There are ways to enable "focus follows mouse" discussed here: 
How can I make focus follow the mouse cursor?, but that might be more than you want...

Otherwise I second MrMojoRisin, get used to cmd+tab or 4 finger swipe (you need BetterTouchTool on Yosemite to bring this last one back).