There isn't anything too complicated about wiring the system up. All of the main power connectors are keyed so that you can't screw it up. The SATA cables are also different and won't fit anywhere they're not supposed to. The only things that can be a little fiddly are the front panel connectors for the power switch, USB, etc, mostly because they are so small. Make sure you consult the mobo manual for proper positioning and orientation.
Now, making the wiring neat is another story. That really depends on the specific case, but in general, you should try to tuck cables behind the mobo tray and use zipties where you can to bundle cables.