The headlights and fan are pretty much a non-issue since they're wired separately and don't pull significant juice through the bulkhead connector. I'd probably do the same with the stereo and call it a day.
They are currently wired to the battery, so they pull juice through both bulkhead connectors and the fusible link when the alternator is working.
In my illustration I show it them connected to the alternator and a direct wire to the battery since that's what he began by asking about.
