Yeah, I found the lack of documentation annoying on the 500R too. Not that I need it, but figures it wouldn't hurt having one. Maybe even a instalation manual (motherboard standoffs, PSU, ect..).
Here's a tutorial on the 650D if you are struggling.
You route the front case cables through the bottom of the case, and plug them at the bottom of the motherboard. For the Extreme4 Gen3, You should have a Audio cable for headphone / mic inputs that plugs at the bottom left of the motherboard, a Firewire port, a USB3 connector, and your bundle of front case headers plugging at the bottom right (power button, reset button, HDD activity light, maybe case speaker connnnector).
They should all be identified on the connector (at least they are on my 500R) and should match headers on your motherboard.
The other 'dangly' cables should then be your front case fans, already connected to the fan controller, with maybe some spare connectors for your side fan and top fans, and a molex power connector to connect directly to the power supply, to provide power to the fans and fan controller. These are best tucked away at the back of the case.