MAD has some really good ideas including the famous Bypass. They also wisely recommend running a distribution point that is fed directly from the alternator. All moderate to high amp draws should also terminate there.
Using quality relays, fusing and wiring is critical. I've found Marine Supply stores carry higher quality components like these in addition to fuse blocks etc. Auto stereo fuses and circuit breakers are large enough to handle hundreds of amps, and I use those sized to my needs.
I also use dedicated grounds to match the positive cables from my alternator, starter, battery in trunk and engine block. power flows equally through both positive and negative. I like the welding supply houses cabling and end fittings, because of its tough casing and super flexible fine strand cables.
