Don't use any Y's. Either run 2 loops or just 1 continuous loop. Like sugar says, the issue with a Y is that if one branch is more restricted than the other the unrestricted loop will get way more flow. Also, if one gets partially blocked due to a kinked hose or build up of sludge, then it will not get flow. If you want to run a single loop and have cool water to GPUs and CPU, then run it ::RES-PUMPs-CPU-RAD-GPU-RAD::
If you want to run 2 pumps you will save your self some hassle and some space by using a dual pumptop. They make them for 350/355s or for 655s and you can get them for single or dual loops. Also, why 2 reservoirs...? The fewer fittings and restrictions you use the better. Oh, and HDD watercooling is pretty much completely useless, but if you want to go for it just for the extreme factor then I approve
I run 2 separate loops with 1000rpm (quiet) fans with a 3x120 for CPU and a 2x120 for GPU. The only reason I did this is so that I can really see how my OC's affect the temps. I was running 2x 5870s, but am now just running 1x 580.
Example of a dual pumptop:
EK-D5 Dual TOP G1/4 - Black Acetal - Pumps Accessories - Pumps & Accessories