@gecko97
Simple Explanation for you, a fan controller is load rated at 50w means it can handle a total fan load of 50w, it does not deliver 50w it allows 50w to flow through it, meaning if the amount of fans you'll be running all together total 60w, then that's too much load for the controller to handle.
If the total fan load is 10w then the fan controller will not be overloaded because the total fan load will be drawing the 10w the fans need to run, and that's all the fans can draw, the fan controller itself does not force 50w into the fans, it does not work like that.
But it will limit the load by use of a variable resistor for each fan, the individual fan control allows full voltage flow or limits the voltage flow the fan can draw and that's how the fan speed is controlled, by limiting or not limiting the voltage going to the fan.
If the fan controller requires 2 molex power supply connections it is probably a safety design splitting the controller into 2 circuits, sharing the load, one molex power supply branch will be just fine to power it.
After further investigation to satisfy my own curiosity regarding your NZXT Sentry Mix Fan Controller.
That's a serious load handling fan controller you have, it has 6 50w individual slide controllers more understandable why it has 2 molex power supply connections, I'm not really sure why NZXT felt the need for such a power load rating 6 50w 120mm fans could probably make your PC hover in the air, and the noise level would be so bad you'd have to be in another room at the other end of your home with wireless keyboard and mouse.
I'm making that statement jokingly I'm sure somewhere on this planet there exists a 12v 50w cooling fan, hidden away and isolated in some hidden room somewhere away from human beings, with ears to hear with.
When I did the Cooling Fan roundup 2012 some fans were eliminated for being too loud to be test candidates and I still have 2 of those fans 12v 120mm x 25mm 20w each pulling 1.68A at 5100rpm rated 58dba, I ran 2 of those at one time and had to leave the testing area.
If those were only 20w what would 50w fans actually be like, as far as your controller is concerned you won't have any problems running the fans you can acquire.