While you will always connect the PS3 controller through System Preferences, the process varies for certain operating systems check your operating.

So now whenever I pair the It will connect but will blink all the time and the bt will say is not connected, but I can play Alien Isolation! However, I have to keep it wired or it will turn. When that app closes, for some reason it stops the lights from blinking. I'm using the controller to play games via OpenEmu. It is an online web-based rhythm game that has controller support.