Now that I read it, I realize that I'm an idiot ... sorry about that. I have a fan controller on my Zalman, it virtually acts as an extension to the 3pin connection on the actual fan its self. For instance, you plug your fan into the controller and the controller into the motherboard.
But, the only fan controllers that I've seen connected to the 3pin connectors ... But, the only machines I've installed them in have the connections on the case fans too.