I've upgraded a bunch of my wires. I ran 4g ground from the stock alternator right under the intake tube to the body. 0g to my stereo system in the ext cab. 4g ground from my large amplifier straight to the battery. 4g + from alternator output to + on battery. 4g ground on battery right to body. I also have an Optima yellowtop. My truck runs smooth, it's a 2001, I don't know if it helped out at all performance wise, but i'm sure it helped with the stereo system. I left all of the stock wiring in, it's real easy to do. I got my terminals at Autozone or Advance auto for like 10$ each.
What size alternator are you planning on getting, and what power are you running for your system?