Your typical surround sound sound card will have 3 audio outputs. One is a Front Left/Right, then a Rear Left/Right, then a Center/Subwoofer. You will not need a 5 channel amplifier. I use a 4 channel amplifier, and plug the Front and Rear outputs to connect to it. Then I plug the subwoofer output to the Mono amplifier for the subwoofers.
To answer the last question. Windows typically plays the rear speakers very quietly. Why it does this, I don't know. But it is more of a home audio setup, rather than a car. It may be more desirable to use a RCA splitter to split the front output to go to front and rear, since that is how headuntis do it.