Help a newb connect his power supply cables to the MSI Z97 XPower AC?

My Background
I am mostly a software kind of guy, and this is my first time building a computer. I saved lots of money, did lots of research, and picked my parts.
So far, I've installed my CPU & Fan to the Motherboard, and mounted them to the case.
Now it's time to install my Power Supply. Mounting it to the case is easy. The problem comes when I have to connect the cables. The manuals don't explain the purpose of these cables or provide "step-by-step" instructions.
I've been searching for over an hour, but can't get a clear idea of what I'm supposed to do. So I'm hoping someone can help me here.
Hardware
Motherboard: MSI Z97 XPOWER AC
Power Supply: Seasonic X-1250
(EDIT: Forum does not let me link to the manuals, so for anyone who needs...please look online)
Problem
On page 29 of my motherboard manual, it shows 4 different power connection slots (JPWR1, JPWR2, JPWR3, JPWR4). Unfortunately, it doesn't explain what goes in them. 
On page 59 & 61 of my Power Supply manual, there is listing of all the key cables.
I think the "Mainboard 24/20 Pin" cable goes into the "JPWR1" slot.
- So I am mostly confused about the other slots (JPWR2, JPWR3, JPWR4).
- Also, it's confusing that there are two CPU cables called "CPU 8/4 Pin" & "CPU 8 Pin".
Can anyone help me? 

Quote from: myfamilyshopping on 24-March-15, 20:00:38
Hi guys, I have a follow-up question about my Seasonic PSU "PCI-E cables".
The way my PCI-E cables are designed is...
There's one end which is a single cable with a 12 hole connector...that goes into the PCI-E port on my power supply.
But then the other end splits out into two different cables, with each having a sort of 6/2 connector.
So regarding the end that splits out into two different cables...
Can each be used on different PCI-E devices?
Or is it the case that because my PSU has 3 PCI-E ports (and 3 of the cables I described)...that only 3 PCI-E devices can be powered?
all can be used however you plan to use them! all them connectors are tied to a single 104amp +12v Rail so they are getting power off a single Rail!
as long as what you plug them into do not exceed the Rail's ratings your fine (would take quite a few Graphics cards to get above that) (basically if it works it works) (would take like 2 R9-295x2's or 4 R9-290X's to get to that point)

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