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Battery wiring setup issue?

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Bought an '89 Tracker TX-17. Had set for almost a year, but was garage kept , winterized and in great shape. Some minor problems I knew about. Depth Finders are at least 10+yrs old and TM one just reads gibberish and vertical lines. Since  I'll be replacing/updating them, I'm not too concerned. Console has a Flasher that works and the other Depthfinder works perfect with it.

However, one thing I thought needed some immediate attention is the battery/fuel area. I get a little nervous with exposed batteries and wiring right next to my gas tanks. So I was putting the batteries in boxes this morning and I decided to check the battery gauge on the console and label the wiring. The switch picks up one battery, but not the other. Switched the wires at the switch and the switch is working must be the wiring for one battery. That is when I discovered that the batteries are reversed. Gas engines are hooked to the Deep Cycle and TM to the starter battery.

Question: Can I just switch the batteries? The TM and Gauge are the only thing wired to the one battery. Do lights, FM Radio and other accessories go to the Starter battery? We had the boat out for a test run over the weekend and it started and trolled fine. We didn't use the 50Hp Merc because of HP restrictions on the lake, but the 10Hp kicker ran fine all day and TM also works fine (MG46lb)

Thanks

On every boat I have ever owned the trolling motor battery was for trolling motor only and starting battery for everything else. I have been told that if you hook electronics to trolling motor batteries a current spike caused by engaging to trolling motor will reset or turn off any fish finders that may be connected to that battery. May cause a premature failure of electronics. You should be safe by just changing batteries............Al

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I kind of figured that radio, lights, etc, would be just like on a car and hooked to the starting motor battery. I should be good to go then. Both batteries test fine, so it appears nothing went wrong. The previous owner and his dad both bought newer boats and I'll bet they just did some battery swapping with this one and maybe got them in backwards.

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