With the graphics card done, it's time to slice up the tubing supplied. The best thing to cut tubing with is a big razor sharp knife; a freshly sharpened Leatherman is perfect. Or alternatively, a freshly sharpened kitchen knife.
The reason you want the knife so sharp is because you want to be able to slice the tubing and leave a fairly clean cut. Raggedy cuts can often lead to leaks and they just look so horrible as well.
First thing is first, mount the motherboard in the case. That way, you know where everything is going to be in relation to the fittings on the board.
Mount your secondary radiator/fan assembly as well. Don't be limited to having it near the CPU either; there is enough tubing to put it anywhere in the case that works best.
The fan can be taken off and refitted in a different orientation, so if you wanted to have the radiator outside the case, that is possible as well
Next, slot your drive bay assembly into the bays you want. Remember that you have to get at the screw cap on top of the unit to fill it up, so leave some room up top unless you have very small hands!
When you look inside the case you should now be thinking of the flow direction; which block leads to which unit.