Care to elaborate on how and why the morphology of a watercooling system would impact factors such as pressure, flow and ultimately heat dissipation ?
I'll take that one...lol. I'm almost scared to think of what might be posted here otherwise...
The order of components in your watercooling loop is important for two reasons. The first and most often recognized, is the heat of the various components that you're trying to cool...in this case the GPU and CPU. You would want to cool the CPU first, as it is generating less heat (in general) than the GPU, and tends to be more reactive to higher temperatures, thus it should be before the GPU waterblock in the loop.
The other factor to consider is flow restrictions of the components you're pumping water through. You want to ensure that you have the least resistance possible in your loop. Hence the references to the diameter of your tubing, and also to your waterblocks. Certain blocks flow water better than others. You may want to look at DangerDen to see what the specs of some of their higher end CPU and GPU waterblocks are (like the RBX or TDX).
So now, the bottom line: what does all this mean to you? With your TT BigWater system, you have neither the flow capabilities, nor the heat removal capabilities to cool both your CPU and your GPU. If you want to do that, you should do one of two things (assuming you want to stick with water cooling for everything):
1: Continue using the BigWater system, but only for your CPU, and set up a complete new loop (pump, radiator, waterblock, etc.) for your GPU cooling.
2: Replace your pump, radiator, and waterblocks with higher-flow variants (stick to 1/2" ID tubing, it's about the smallest recommended size for any kind of heavy duty cooling).
Bottom line is that the TT BigWater is just not capable of cooling a CPU and GPU, even less so if the GPU is something fairly recent (or fairly OC'd). If you need help choosing new components, just post back and I'm sure some of us forum junkies can help you out.
-J