Wiring
Nothing is more frustrating than getting your system all put together only to find out that none of your LED case lights work or any of your front case USB ports work either. There are a couple other jumper settings that may have come from the factory set incorrectly as well. I will try to explain how these USB/LED and jumper connections should be made. The examples below are from my Lian-Li PC 75B case, but should hold true for most newer cases out there with front USB connectors, and LED power and IDE activity lights.
FPIO1 Connections
The first thing we will cover is the case switches and LED's for the front of your case. The biggest problem people have is figuring out which direction to plug the headers onto the motherboards FPIO1 pins.

As you can see by the picture above, you can easily tell where to plug your wires to, but its not much help as to what direction. Take a look at the picture below, it will show you how all the connections are made as well as the proper orientation. The connector under the POWER SW that you cannot read is the RESET switch connector and the one under the POWER LED is the connector for the case speaker. In the illustration below you can see that all my positive (+) connections are to the left, and of course all the negative (-) connections are to the right. Follow this picture and you should have it right the first time!

FPIO2 Connections
The FPIO2 connectors are used for different functions of the onboard soundstorm. There have been cases of the motherboard being shipped from the factory with these jumpers in the wrong position. You should have a jumper on the 5/6 pins and the 9/10 pins for normal operation. See the two pictures below for how it should look.
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USB 1/2 Connectors
The USB connectors can be very frustrating at times to get working correctly. Some times you get lucky and the wires are all together in a Molex connector and you can simply plug them in. More times than not you are left with a bunch of wires that need to be plugged in one by one on the proper pins. Take a look at the pictures below, they will show you what each pin is for and how I have my front panel USB connections hooked to them.
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Sometimes all your wire connectors are labeled according to the diagram on the left above. If this is the case then hooking them up is pretty easy, if they are not labeled, then you should be able to follow the color code as in the picture on the right above.
Clear CMOS Jumper
In order for the motherboard to work correctly the Clear CMOS jumper must be in the correct pin position. Again there have been reports of the jumper coming from the factory with the jumper in the clear position. Make sure the jumper is covering pins 1 & 2 before you start your computer for the first time. The picture below shows the jumper in its default position needed for proper operation.

If the need arises where you need to clear the CMOS, then of course move the jumper over so it covers pins 2 & 3. Remember to replace the jumper back to pins 1 & 2 before restarting your computer.
Hopefully this section will aid in setting up your connections and jumpers correctly the first time!