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Did some more research, looks like there are some pre-made IC's that will operate as power switches with easy wiring and setup and low on-state resistance (low heat generation while current is flowing through), rated up to currents that would be OK for us in the car's electrical system (steady state about 100 amperes, surge current up to about 200).
They cost about 8-10 bucks each at digikey and have all kinds of neat features like resistance to ESD, current limiting, and protection should you wire it backward.
Well worth not screwing around essentially making our own version of that IC, that's probably what I'll use to separate the power supplies. Two of those attached to a switch in the cabin should allow one to toggle between the panel and the alternator as required (if system voltage starts to drop when using the panels, switch to the alternator to get it charged back up again). Could probably be combined relatively easily with the switch that would be required for an alternator disable, as you'd want to disable the alternator while it can't put any power through the switch.
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