You shall find flexible SLI connector inside Your Maximus VI Formula motherboard box. Check my gallery how cards should be put into PCIE slots (first and second slot).

Cool, thanks. I'm running EVGA GeForce GTX 780 Ti Superclocked GPUs, well, once I add the 2nd one I will be. I have a waterblock on the card I'm using now and intend to add one to the new card. I have the SLI bridges, but I kind of like the way the metal one by Nvidia looks, not to mention that I need to get an EK bridge. Would you suggest I run them serial or parallel?

Please consider me as a totally novice in watercooling as I did my first build, it probably depends from Your other water blocks and pump, in my case firstly I cooled only one card and CPU because EK messed things with backplates - one I received was for 780Ti Matrix and second one I received was somehow for Matrix Radeon, plus I ordered wrong Terminal (2-slot) by mistake, but I personally use EK-FC Terminal DUAL Parallel 3-Slot and temperatures compared to GPU+CPU for me after adding second GPU + CrossChill is same as it was with one card. Maybe it's not lowest You could expect from water cooling but I'm getting 49C GPU temp / 56C VRM on first card and 46C GPU temp / 54C VRM on second with quite high overclock - 1337 GPU boost while playing for long period of time in Battlefield 4 MP with V-sync off. Temps on first card are same as when running only single card overclocked.

I installed the second card, hooked up the SLI bridge that came with the MB, but the 2nd card isn't being recognized. Is there anything I need to change in the BIOS as far as the PCIe slots are setup or should the MB automatically recognize the 2nd card? When I first turned the PC back on, it downloaded another Nvidia driver, which made me think it probably recognized it, but the driver is slightly different. However, if I open the Nvidia Control Panel, according the the information I've read, there should be an option to select SLI configuration under 3D settings, but I don't have that option. I have both cards installed (2-780Ti Superclocked) in PCI slots 1 & 2, and I have the additional 6 pin power adapter and the additional 8 pin power adapter hooked up to each card.

Just out of curiosity, I went into the BIOS where it shows what type of memory chips are in the DIMM slots and what kind of cards are in the PCIe slots, and it only showed 1 GPU (the original card) in slot one. It did say it was running at 8x instead of 16x like it usually does which tells me the MB recognizes the card, but it's not setup correctly. Any suggestions?

The bios should be recognizing your second card. Do you have the pcie cables connected?

Try reinstalling the NVidia driver, let the sli connector connected.

Do a custom/advanced install and check the box that says perform a clean installation.

Yesterday, I ended up draining my waterloop, removing my original card,and installing the new card into slot 1 and it worked fine. One thing I noticed, this new card has the EVGA ACX cooler on it, which makes the card a little bigger on all sides. My MB has the ROG armor on it, and when I try seating this card, it's a tight fit. The bottom of the card, which is basically part of the cooler, comes in contact with the armor. This might be preventing a proper seating of the card in slot 2, especially since I have a waterblock on the Z87 chipset, which is right between slot 1 & slot 2. If this is the case, once I put a waterblock on it, the size of the card will be much smaller.

Sounds like it's getting a bit complicated, keep things simple.