I finally got around to upgrading the underhood wiring on my Civic. It's not that difficult, and should take a handy person a few hours to do it cleanly - start to finish.
So, let's first talk about what the magic 3 are, and why we upgrade them. There are three wires in your system that are vital to charging system performance:
1. Positive lead from alternator to battery
2. Ground from battery to chassis
3. Ground from engine to chassis
Factory charging systems were not designed to supply current to aftermarket accessories, such as amplifiers. The factory also cheaps out on the wiring, using the minimum effort and raw materials to get the job done.
When we start talking about choosing wire size, there are a few things to keep in mind. All wire has resistance - no one has made the perfect wire yet. When we think about passing current across a resistor, we will experience a drop in voltage from one side to the other. In our cars, it's important to provide our amplifiers and accessories with as much voltage is possible (for those of us with loosely regulated power supplies especially

).
As wire diameter increases, it's resistance decreases. So when picking a size wire, generally, we decide on an acceptable voltage drop for that run of wire. Then we look that current (measured in Amps) that the wire must transfer. Then, take a look at the length of the run. After these parameters have been examined, we can choose a wire of the appropriate diameter. Keep in mind, as the length of the run increases, the wire's ability to carry current decreases (keeping all else equal).
So with that booooorrring primer on basic physics of electricity, here's how to replace that Magic 3 in your car: