Cooling Setup: How am I supposed to hook up these fans? 2 front intake, 1 rear exhaust, & Kraken x61 on top

I agree with Aeacus re the Kraken fans. However, I suggest you should not connect any of the three other fans to the Kraken pump sockets. Those are designed to power optional extra fans on the Kraken radiator and are guided entirely by the cooling needs of the CPU chip.

You are fortunate. Your mobo has two CHA_FAN headers and each is completely able to adjust to your fans. First point is this: using a simple Splitter you can connect 2 or 3 fans together to a single mobo fan header. With all common fans this will not overload the header. I'd suggest you use one splitter to connect both front intake fans together to one of your CHA_FAN headers, and the rear exhaust fan to the other header. You have not told us what type of fans you have - that is, 3-pin or 4-pin. But I'm assuming that at lest the two front intake fans are the same. This is important for setting each header's control mode because you cannot control a 3-pin fan using the PWM Mode.

So here are details. First, get a simple splitter that makes a single mobo fan header into two, like this:

http://www.newegg.com/Product/Product.aspx?Item=N82E16812423161&cm_re=coboc_fan_splitter-_-12-423-161-_-Product

This is actually a 4-pin splitter, but it will work both for those and for 3-pin fans. As a side note, this splitter does what it should - it feeds the speed signal of only ONE of its fans back to the mobo for display. The other fan on this splitter will have its speed signal ignored, and you'll never see it.

Connect two similar fans (both 3-pin, or both 4-pin) using this to one of your mobo CHA_FAN headers. Connect your third fan to the other. Now boot into BIOS Setup to set the header configuration. See your manual on p. 2-36, Section 2.7.6. Set each header's "Chassis Fan Q-Fan Control" to either PWM Mode for 4-pin fans, or to DC Mode for 3-pin fans. For both set "Chassis Fan Q-Fan Source" to "MB". Leave the Low Speed Limit at default unless you find a need to change it later. Set the "Chassis Fan Profile" for each to "Standard" so it will use automatic control. When you've made the changes here, remember to SAVE and EXIT.

This will put all three of your case ventilation fans under automatic control governed by the temperature measured by a sensor built into the mobo by its maker.