One at a time
Some people have posted that they run with both batteries on. I would never do that. I run one battery one day and the other battery the next time I use the boat.
The potential problem with running on both is that if you have a major short or electrical problem you lose both batteries.
If you run on one at a time, and your voltage regulator fails and overcharges, you only fry one battery. If you run on one battery at a time and your charging system fails, you still have a fully charged battery in reserve. When running on both batteries the potential for two dead batteries and nothing left to power your bilge pump is also there. If you kill both batteries at night you will have no lights.
One battery at a time works fine for me! I like the security of having a battery in reserve.
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