As you have a "pain-in-the-***" harness, it's probably not quite setup like that.
You'll want a fusible link on the feed from the engine compartment to the fusebox. (the 16 gauge fusible link shown in the diagram above)
and in the positive "pigtail" lead on the battery cable (the 14 gauge fusible link shown above.) If you use reproduction spring ring battery cables, this fusible link is part of the cable.
Fusable links should be installed as close to the power source as reasonably possible. Alternatively, the power stud on the starter can be used as a subsystem power feed. Keep in mind that fusable links are meant to burn in two, so don't put the fusable links in a place where they'll melt or burn things you don't want to burn or melt.
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