When cooling your components by water cooling a single loop will only go so far and there will be components that won't get the same cooling power as those at the front of the loop. Some will suggest to put two or even three radiators spacing them in between the different components. That would be fine provided you get a pump strong enough to push the liquid through all that and not burn out from the extreme work load.
Don't forget each radiator and block provide some level of resistance to get the liquid through it and too many components providing too much resistance will over load the pump.
The solution would be to have multiple loops and while it will be expensive those that opt for custom water cooling are already willing to accept the cost. Also this doesn't have to be done all at once and you can build the system over time adding sections as you can. This is custom and adding is never a problem it just takes planning.
In this picture we see that the CPU , two video cards, two sets of Ram (one on each side of the CPU) and the motherboard chip set plus power regulator all cooled by two loops.
To make a two loop system.
There is different ways to do it but for this way we will treat it as two separate single loops. So you will have to decide what components will be cooled , what you plan to do for overclocking and how do you want it to look. Do you have a side window and want every thing to look nice and neat? Do you have a color scheme that you want to keep the same.
In doing the same as the picture above and cooling the same components you want to draw up the loops on paper first and that way you will eventually have a blueprint to follow and this will eliminate any forgotten parts or direction.
The two most important components will be the CPU and the Video cards so these will be split between the two loops and they will be the primary places to cool on each loop. The Ram and the motherboard are not as important so they will be secondary places to cool on each loop.
When doing a multi-loop set up be prepared to have something mounted on the outside of the case or somewhere near the case outside of it. Space becomes a premium on the inside of a case when adding radiators, reservoirs, pumps and tubing and even the super towers can come up short on space when too much is added.
Underneath the top of a desk can serve as a pump and radiator platform if needed.
Shopping list. If starting out new and you want to build both loops at the same time then your going to have a big shopping list and with that many parts to order you will most likely forget something. So with that in mind there is no reason to rush so check the list over several times while looking at your diagram to make sure. Forgetting something small would not be that bad but you want to make sure that you are correct on the bigger items.
a. Two radiators, preferably 360mm
b. Two reservoirs, getting the front bay type that includes the pump would save on space but you'll need four bays.
c. Two pumps, this will be the better option as you would be able to get the single bay reservoirs or the tube style.
d. Enough tubing plus a few extra feet just in case.
e. Liquid, again enough to fill both with some extra.
f. Fittings, this is where you can slip up and not get the right amount.
Connecting your loops, this should be done one loop at a time as if you were installing a single loop but keeping in mind that there will be the second loop so not to block something off. The primary component of each loop should be the first thing connected coming from the radiator so that it gets the coolest liquid. This is especially true when it concerns the CPU. So connect the CPU first then from the CPU connect the motherboard block then to the pump and then the reservoir. The second loop will come from the radiator to the first video card then the second video card and then to the Ram blocks, then to the pump and back to the reservoir.
Each loop should have a fill port provision and a drain port provision.
Fill and test the first loop and then fill and test the second loop, once they are both full and tested for leaks you can then run the both loops for an extended period of time to get the rest of the air out and to further check for leaks.
The same procedure should be followed as explained out in this tutorial on filling and maintaining your loop. Don't forget the biocide treatment.