The outputs on the PolarFLO may be arranged in many ways. As long as you do not choke the flow on either of the outputs more than would occur if both outputs were combined into one line. The flow design was made to allow the two outputs to be plumbed back into one 1/2" ID line. Choking it any more than that will adversely affect performance. Presumably if you took both outputs and put them each directly into the reservoir, one may see a small increase in perfomance.
Good luck on your project, our GPU/Chipset water blocks will be out soon.
Best to all.