General Power Supply Question

I wanted to know how to evenly distribute the load on my power supply? I have a corsair 1000w which has 2-12v rails at 40A each. According to the manual 4 pci-e connectors are on one rail and everything else, including two hardwired pci-e connectors, is on the other rail. Since I have two 4850's which require 1 pci-e connector each, I just use the hardwired ones. My question is should I use two modular pci-e connector that is on one rail for the video cards and let everything else go on the other rail, use one modular on one card and one hardwired on the other card, or do what I'm doing now which is use both hardwired pci-e connectors on each card. By doing the latter doesn't that mean that everything in my system is on one rail and essentially only have the potential of using 500w? Please help me understand how to correctly use not only my power supply but power supplies in general that have more than one rail