If you aren't using the 2nd 5.25 bay and want a solid fan controller, I would look at something like this. All you need is molex power plugged into it and you can control them individually.
Its kind of pricy at $60.00 but its a very solid controller for basically any fan you want to put on it.
Or... if you want something else, there is a variety, but these kinds of controllers make it easy if you want to adjust on the fly without software.
Personally I use this and just let the fans run and max speed, but I don't care about the noise, more the coolness of the case.