bump, any ideas?

Its going to be annoying;
 
The CLEARCMOS switch is wired for a 3pin header where there is a "Normal" position and a "Clear" position.  You'll need to figure out which pin on the 2pin connector is the common for the reset switch's 2 positions - it should be pin 2.  Once the common pin is found, you connect it and pin 3 to your Gigabyte's CLEAR CMOS header.
 
~Fus

The motherboard does not come with a jumper believe it or not (I guess I can, $530 board didn't even come in an anti static bag nor do the RAM slots have that nice sticker over them to protect from any dust particles like EVGA's do lol).
 
From reading the literature, I got the impression if connected improper, it could damage the motherboard.
 
Here is the manual: http://www.silverstonetek.com/downloads/Manual/Multi-CLEARCMOS-Manual.pdf
@dhemke, The motherboard only has 2 pins for the clear cmos, not 3. 
@Fiius, You are saying pin 3 will be used and I will use half of the 2 pin part? Here is the manual's table on the pins.

I appreciate your patience and thoughts. I am still working on my case and preparing to finish my build. I am not quite ready to connect everything, I am just trying to get informed before I get there.

Wow, what a joke, took forever to dwnld 34 pages of your manual. Gigabyte needs a faster server.
 
2 pin Clear CMOS, no probs, forget the number "3" connector, it's useless to you, not needed at all in your situation.
 
Anyhow, with the jumper off, your mobo/CMOS is in "normal" mode, jumper on it clears.
 
Too easy. The switch is set up for a 3 pin mobo, so no matter how you look at it, in one position the switch is closed between the contacts labelled 1 and 2, in the other position it's open. Orientation of the connector on the pins does not matter, this is a simple switch, it is either OFF or ON, polarity is not an issue. I can assume which is which, but let's not do that, $350 assumptions are not all that bright.
 
Grab a multi-meter/ohm-meter, place a probe in each of the switch's connectors, as in one of the probes in "1" and the other in "2".
 
Set your meter to ohms/resistance.
 
It does not matter what the label on the switch says, when you have ZERO resistance, the switch will be set to Clear CMOS in reference to your mobo. Mark the switch as such, so you don't forget.
 
Move the switch to the other position, you should have INFINITE resistance, that would be NORMAL in reference to your mobo, mark the switch as such.
 
Move the switch to NORMAL, as in the position you marked as "normal" on the switch. Connect it to the mobo. You're set to go.
 
When you need to clear the CMOS, shut down, turn off the PSU switch, push the power button on your computer(fans will probably spin briefly), disconnect the power cord from the PSU, move the switch to where you marked it as CLEAR CMOS. Leave it there for whatever amount of time your manual suggests(probably 30 seconds or so), set the switch back to "normal", and you're done.
 
Piece of cake. This WILL work.