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Ron, I don't know what you've got, but one wire may be a voltage sense lead. that goes from the alternator to the one battery, so the alternator can monitor battery voltage and regulate itself. On some systems, the sense lead is tied back right into the alternator output (which defeats the purpose) because the boat has 2 batteries and it costs more to switch the sense lead when you switch batteries. If you bypass it, that's called a "one wire" installation versus a conventional "three wire", some boats are set up that way because it is cheap.
You don't have to set it up the way the maker did, there ARE options. But you do need to make sure of what each wire is, preferably from a schematic confirmed by tracing them out to make sure someone didn't monkey with them. Maybe someone in the forum has the same make boat you do--and can comment on how it was set up.
An idiot lamp is usually connected to the "field" wire, which supplies twelve volts to "excite" the alternator and start it up. On a "1 wire" system that's usually tied back as well, with the side effect that the alternator doesn't fire up until a certain RPM is reached, often meaning you need to "goose it" to get it started.
The voltage sense lead can be critical--if it is not connected to anything, the regulator says "MORE POWER!" and often goes to 17 volts, quickly frying everything. So...take your time, make sure of what everything really is, not just what it is supposed to be.