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Wiring set-up for battery switch.
Depending upon the electrical equipment you have on the house load, you don´t want the starting battery to draw the voltage being supplied to your radar or Gps, or whatever. Even if you have a high amp rated starter battery, with the kind of 1,2,both, off Perko switch, by the time you connect the #1 starter battery, you do also supply voltage to the house load. When you start the engine, you will find a huge voltage drop in the electric supply to the house load. The more old the battery higher voltage drop. The inmediate result in some equipment is the reset or restart, case in Radars or 12v GPS. Some other equipment may harm.
In addition, nothing happens at the departure on dock. But when you are negotiating the access to certain ports, with bad weather, and decide to star the motor, the last thing you would probably like is to reset your instruments.
For that reason, some people hardly recommend having two off-on switches and a third one to paralel both batteries just in case. With this arrangement you can isolate completely the starting and house load systems.
In the case of your Yanmar, as SailorMitch suggets, you would´nt need a high amp starter battery. Probably a standard one is enough. Particularly considering that the engine has decompressors that will allow the starter motor to run even with very low battery. However, the theory for always having a good battery to start the engine, is to use the starter battery only as starter battery, and the other one for house loads.
If you find from time to time, the starter would not kick in you should check tightness & cleaneness of connections first. But more important, is to be sure that no water is inside the engine. Sometimes, the flowbak or siphoning might let water inside the cilinders. Particularly is an exhaust design problem. If that might be the case, you should decompress the engine at the ignition, and after a couple of turns, put down again the compression handles. This will allow any water in, out the exhaust.
Lastly, you did measure the altenator output as 13.5 volts, where, at the batteries or at the alt output. In any case, at 2.000 RPM the figure should be greater, at least 13.8 v.
You might want to review some introduction on electricity matters in th Westmarine page :