Where do I plug in these fan cables?

[t0pher]

Unfortunately my case and motherboard (Fractal Design Define R4, ASRock B85 Pro4) didn't come with any instructions so I'm wondering where to plug these in.

Here is a pic of a few cables coming from the front of the case. The left connection looks like it matches up with something from the PSU. The 2 smaller right ones look like fans can plug into them. What is each of these doing? (There is an additional shorter cable that looks like the smaller one for fans that is behind the back panel.)
http://i1141.photobucket.com/albums/n587/decembertopher/2014-03-30152818.jpg

Here is a pic of the back fan. My computer has an identical fan in the front of the case. Would these both plug into the two ports from the previous picture?
http://i1141.photobucket.com/albums/n587/decembertopher/2014-03-30153040.jpg

Here is a pic of the motherboard section for fans. Considering there's only one 3 pin connection and I have 2 fans, I would think I should plug the fans into the 2 ports from the first pic.
http://i1141.photobucket.com/albums/n587/decembertopher/2014-03-30153850.jpg

I have a fan speed controller on the front of the case. Which cable is controlling this? I think I know where all the other cables from my case are plugging into the motherboard (USB 3.0, USB 2.0, power button, reset button, led, HD audio).

 

[clutchc]

First pic is the wires from the fan controller. The big one is the feed that plugs into any matching connector from the PSU, the small ones connect to the case fans.

Last pic: The CPU FAN header is where you plug in the fan that is on the CPU cooler. The other header can be used to plug in any 3 pin case fan. But since you are using the fan controller, ignore it. Or use it if you ever add another case fan.

You can get the MB manual here: http://www.asrock.com/mb/Intel/B85%20Pro4/?cat=Manual
You should have it on hand for reference.

You can get the manual for the case here: http://www.fractal-design.com/home/downloads