Stereo install

I have never installed a quality stereo system in a car before. Is it better to box all speakers? What determines the size of the box? I know a little about resonance, but how does it relate to the size and shape of the boxes? Should mid and high range speakers be aimed at the listener or does it not matter as much inside a car? What does one look for when shopping for speakers, power amps, radios, etc? How about wires? Antennas? It seems that the most modern stereos use a computer port for some sort of download. Is that for an ipod or a memory stick?

Man, I hope all these questions don't bother you guys too much, but I am a self-confessed electron moron.