I have had this issue on another EVGA board the x58 SLI. The only thing I can recommend is getting a PCIe sound card

What Bios are you on? If not I would recommend that you update to 2.04
I have not seen any Audio issues on the FTW or any other EVGA X79 MB.
Reset your Bios and then set it Optimized and reboot and check that the Audio is enabled?
 
Current Bios: 
12-19-2013 BIOS 2.04 151-SE-E777 Win8/Win7/Vista/XP Download View
Once on this version you can take pictures of your Bios settings and save them to a USB Thumb Drive.
 
Current Audio Driver: 
11-21-2013 AudioR 2.73 151-SE-E777 Windows 8/8.1 64bit Download                    

Un fortunately due to space restrictions in my case I cannot move my card down any further, nor am i able to connect the extra PCIe sata connector on the bottom of the mother board. Could the card being on the wrong PCIe bus possibly be causing these issues?
 
I do remember seeing a review, I believe on newegg, where someone said the board worked fine until they added a 2nd videocard...hmmmm...
 

If I were you I would RMA the board. If the new one has issues then I would sell it and get a better board. Usually I stick with EVGA but recently their motherboards have SUCKED

I completely forgot about the little 1x PCIe thats hidden behind my video card, so I stand corrected, my video cards are in fact in slots 1 and 5. My usb seems to be working again after disabling some of the power save features on the board, but I will check those links you provided. And now when I get home i will double check the front audio header to ensure I have it connected properly. 
 
On a side note, why did I have to manually set the board to PCIe 3.0, and also why is PCIe slot 1 only running at 8x and the second one is running at 16x, despite the fact that I set them both to 16x? Also I have no other PCIe cards in this system, only the 2 graphics cards.

Nope, Slot 1 is running at 8x, and Slot 5 is running at 16x. I don't understand it because I have no other cards installed. 

Ok, Ill do that when I get home today. 
 
My PSU, If I remember correctly its the Thermaltake SMART M Series SP-850M. its a modular 850W. 
 
Also, does anyone have any idea why my USB stops working when I overclock? this is the weirdest thing I've ever seen...I can literally bump my turbo multipler up just 1 tick, and my usb stops working, i put my cpu back to stock and my usb works fine O_o Also I did install the new USB firmware, that was suggested, it didn't really make a difference, but it never hurts to update. :D
 
I have given up on the onboard audio, I just ordered a ASUS Xonar U3, so im not worried about the audio anymore.  

 
Heres a snapshot of my config for my PCIe slots. As you can see I removed the 2nd card and have the 1st slot manually set to 16x yet it still says 8x at the top.
 
I have since switched over to bios #2 which is still flashed to an older bios, and I still have the same problem with the graphics running at 8X, and with spotty USB3.0 ports, but I now have my overclock back. 
 
So my full situation seems to be;
1. My primary graphics only runs at 8X (even when 2nd card is not present), however 2nd card always runs at 16x
2. My USB 2.0 ports work fine, however my USB 3.0 ports are spotty and require several reboots to work properly. 
3. My on board sound does not work at all and never has, this is a non issue, I disabled it and ordered a ASUS Xonar U3.
4. I can only achieve a stable overclock on the older bios, the new bios(the one in the screen shot), will not give me a stable OC. (infact the OC you see in the screenshots caused a BSOD on reboot.)
5. I have the USB debug sounds enabled, I call it the R2D2 boot sounds, and In the old BIOS everything works fine, on the new bios I started to not be able to post, it hangs on 9C and just beeps constantly, sometimes it would sit there for 20 or so seconds then boot, sometimes it wouldn't. (this seems to be a new problem only occurring since yesterday, I do not have this issue on the older bios, only the new one.) 
 
I have since changed my Power supply to my trusty Corsair GS800, and I have situated it in such a way that I now have the bottom molex for additional PCIe power connected. It has made no difference what so ever, and I don't see any options pertaining to the additional power connector in the bios. The only connector I cant hook up in the 2nd 8PIN power connector by the CPU, which is even referred to in the manual as optional. Considering I have one of the lowest power CPUs avaliable for this board I don't see how not having that connected would be an issue. However I can always order...or make an 8pin splitter so that I can connect them both.  
 
I greatly appreciate all the help.

relink2013

 
Heres a snapshot of my config for my PCIe slots. As you can see I removed the 2nd card and have the 1st slot manually set to 16x yet it still says 8x at the top.
 
I have since switched over to bios #2 which is still flashed to an older bios, and I still have the same problem with the graphics running at 8X, and with spotty USB3.0 ports, but I now have my overclock back. 
 
So my full situation seems to be;
1. My primary graphics only runs at 8X (even when 2nd card is not present), however 2nd card always runs at 16x
2. My USB 2.0 ports work fine, however my USB 3.0 ports are spotty and require several reboots to work properly. 
3. My on board sound does not work at all and never has, this is a non issue, I disabled it and ordered a ASUS Xonar U3.
4. I can only achieve a stable overclock on the older bios, the new bios(the one in the screen shot), will not give me a stable OC. (infact the OC you see in the screenshots caused a BSOD on reboot.)
5. I have the USB debug sounds enabled, I call it the R2D2 boot sounds, and In the old BIOS everything works fine, on the new bios I started to not be able to post, it hangs on 9C and just beeps constantly, sometimes it would sit there for 20 or so seconds then boot, sometimes it wouldn't. (this seems to be a new problem only occurring since yesterday, I do not have this issue on the older bios, only the new one.) 
 
I have since changed my Power supply to my trusty Corsair GS800, and I have situated it in such a way that I now have the bottom molex for additional PCIe power connected. It has made no difference what so ever, and I don't see any options pertaining to the additional power connector in the bios. The only connector I cant hook up in the 2nd 8PIN power connector by the CPU, which is even referred to in the manual as optional. Considering I have one of the lowest power CPUs avaliable for this board I don't see how not having that connected would be an issue. However I can always order...or make an 8pin splitter so that I can connect them both.  
 
I greatly appreciate all the help.

I don't really know that much about the X79 FTW, but is your ram all supposed to be lined up on one side like what shows in your pic??  NM...I see now there is only 4 dimm slots.

relink2013
I have tried setting the PCIe to auto and it still doesn't work.
 
As far as the audio goes, it was enabled and it didn't work. I have it disabled now because honestly I just done care about the audio, lol.

Cool,
You do know that the cards you have are Gen 3 Cards, so if you can or are able to I would RMA your Motherboard.

Im going to call EVGA tomorrow and find out what I can do. Does anyone know where on the board I can find the serial number? The tag is not on the box.