Need help understanding the buyer's guide

It's not easy to understand, but maybe this helps: http://www.enthusiastpc.net/articles/00003/2.aspx
And a nice picture here: http://www.intel.com/content/www/de/de/chipsets/performance-chipsets/z97-chipset-brief.html?wapkw=z97+product+brief&_ga=1.118826189.514717540.1430924399

Its simple. Any Intel 1150 socket based CPU, only supplies 16 PCIe lanes. So the motherboard designers have to live with that restriction. So what they do is this.

1 video card: Goes in slot closest to the CPU, and gets all 16 PCIe lanes.
2 video cards: First card goes in slot closest to the CPU, and the second card goes into the next closest 16x slot. Each card gets 8 PCIe lanes.

This is good enough for nearly everyone.

If you really do want more PCIe lanes, and are willing to spend extra money to get them, you can move up to a 2011-v3 socket motherboard, and get the $1000 CPU (I7-5960X) or the $570 CPU (I7-5930K), and get 40 PCIe lanes. But you also have to buy a third party CPU cooler since those CPU's do not come with a cooler or fan, and those CPU's only support DDR4, which is more expensive than the DDR3 that the 1150 socket based CPU's use. There is also a I7-5820K CPU for the 2011-v3 socket motherboard that comes with 24 PCIe lanes. It runs about $360.

This is a small sample of motherboards that support 2 video cards, 3 slots apart. There are lots more than what I have listed here. I have provided links to each of those companies so you can see what I was looking at to find these. The models I list do have 16x PCIe slots 3 slots apart based on the images the companies displayed on their website. Again, there are many more motherboards at each company like these.

Asus Z97 Deluxe (various models)
Asus Z97 Pro
Asus Z97-A
Asus Z97-C
Asus Z97M Plus
Asus MAXIMUS VII FORMULA
Asus MAXIMUS VII HERO
Asus SABERTOOTH Z97 MARK 1
Asus SABERTOOTH Z97 MARK 2
Asus Z97-WS
http://www.asus.com/us/site/motherboards/Z97/comparison/

MSI X79A-GD45 PLUS
MSI Z97A GAMING 7
MSI Z97 GAMING 5
http://www.msi.com/product/motherboard/#?category=Socket 2011&category_no=966

AsRock Z97 Pro4
AsRock Fatal1ty Z97 Professional
AsRock Z97 Killer
http://www.asrock.com/mb/index.asp?s=1150

Gigabyte GA-Z97P-D3
Gigabyte GA-Z97X-UD5H
http://www.gigabyte.com/products/list.aspx?s=42&jid=0&p=2&v=31

Now on to [strike]Future Proofing[/strike]. There is no such thing as [strike]Future Proof[/strike] in computers. The industry moves way to fast to even consider [strike]Future Proofing[/strike]. The best you can hope for is to get 2 to 5 years out of most of your hardware. Right now, what you buy today is going to be outdated in a year. New CPU's from both AMD and Intel will require motherboards with new sockets that are not even out yet within 12 months. Memory is moving from DDR3 to DDR4. Video cards next year will be much faster than anything out there today. About the only thing we can count on as being [strike]Future Proof[/strike] are the electrons that make our computers function. And even those will eventually be replaced with photons and/or Quantum Physics.

Now to water cooling. I know what they are. I know how they work. But I have never been real comfortable putting anything containing liquids into my computer. So I have never used water cooling. Millions of people are comfortable with this, and I have nothing against it. But since I have never personally used water cooling, I am going to stay out of the discussion on it.

Finally game software. Since you mentioned Arkham Knight, I will start there. The Arkham Knight port of the game to the PC was absolute and total crap. It was so bad that just days after it was released, Warner Bros, pulled the PC version off of the market, and offered refunds to anyone that wanted their money back. They promise to fix the problems, and re-release it. We will see. So forget about Arkham Knight for at least a while.

Now, it appears that game developers are aiming for 4K and above resolutions already. Which in my opinion is good and bad. Good in that the games will look fantastic on a 4K monitor, but bad that they are not as optimized for the majority of us that do not have 4K monitors, and probably will not have 4K monitors for a few years yet. So what is happening is that the new games come out, and its hard to get a steady 60 FPS in any of them at resolutions most of us have, and even people with $650+ video cards are having problems maintaining those numbers at times. So most of us have no chance of steady 60 FPS without dramatically lowering settings. You will still see some issues with 60 FPS in some games at Ultra and Very High settings even with an SLI setup like you are talking about. Sure, you will be better off than most of us. It still will not be perfect.

And finally, overclocking. To be honest, its not what it used to be. As CPU node sizes have gotten smaller, the heat is concentrated into a much smaller space because the CPU itself is concentrated in a much smaller space. That makes it harder to cool, and as a result, harder to get big overclocks out of. GPU's are also headed in the same direction. For the last 4 years, both AMD and Nvidia GPU's have been frozen at the 28nm process because the 20nm node never developed the process technologies both companies needed. Starting next year, both companies will be moving forward to 14nm/16nm GPU's and the heat from the GPU will be concentrated into a space very similar to the space the Intel CPU's are facing now. So overclocking anything by much is becoming harder, and less beneficial. You can put a whole lot of time and effort into overclocking, and only see a 2 to 5 FPS increase. Or none. Depending on the game, the silicon that is your CPU and GPU, and other factors.

And finally, Using dual 16x PCIe 3.0 slots at 8x electronically will produce higher frame rates than using a single 16x PCIe slot at 16x electronically. But it will not be double the number of frames in most or all cases. Normally, it is anywhere from 50% to 80% increase, but a lot depends on the game, and how well it was optimized for SLI/Crossfire. Some games simply do not so SLI/Crossfire. Others do, but with very minor increases in frame rates. And then the ones that were designed from the ground up to support it, can often almost double its frame rates in SLI/Crossfire modes. There is no "One Shoe Fits All" here.