Having two rails means you have two different 12vdc regulators providing power to your system. Typically, one rail will power your motherboard and video card, and the other handles the peripheral devices.
This accomplishes two things-- one, your motherboard's power will not be affected by sudden load changes caused by peripherals such as CDROMs spinning up to read. Second, using two smaller-amperage regulators is more efficient and creates less heat than using a more robust high-amperage regulator.
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