And I like drawing diagrams of what I'm always talking about, but I'm really, really bad at it! Wish I was better, or would just take the time to figure out the use of a computer program like Paint or something so I could make more sense. ;D
For locations of components, that's left up to you in most cases, since you're completely modifying it from original, you get to choose the cleanest routing to take.
For instance, I ran a friend's alternator cable all the way back across the intake manifold, down behind the engine and across the firewall down low, then back forward to the battery along the main harness on the inner fender apron. It's longer and more convoluted, but we just didn't want to take the shorter route that most do (and I've done too) of straight from the top of the alternator over to the fender.
Works either way, but whatever suits your fancy is often the "best" way.
Notice the Mega-Fuse holder along the wall there. The EFI fuses and relay pack are along the firewall just behind that.
That's 2ga cable at the battery and 4ga for the alternator. We've since gone to the cleaner looking "military" square lug battery connectors.
The big Radio Shack type of terminal strip is taking the place of the junkyard GM truck buss-bar while waiting to cut it into three separate isolated sections. One is CONSTANT power, one is SWITCHED power, and one is power in START only.
For some confirmation of recommendations, Ford uses 6ga on their cars (and maybe some trucks?) that have shorter runs from the alternator to the battery (or load center) and 4ga on the longer runs. Lots of trucks and vans especially have the 4ga setup.
Ford even uses Mega-Fuses on some applications, while still keeping to the fusible link protection method on others. The fusible links are often visible as a shorter run of two much smaller gauge wires connected to the single larger gauge wire.
Paul