From the day I bought Rainbow Chaser, I didn't like the battery switch and all the problems that came with it. The solution I came up with was to add a second alternator. The starting battery is charged by the small original alternator that came with the Yanmar, the house bank is charged with the 150 amp Hamilton Ferris unit.
Between the two banks is the old switch. The switch now needs only to be changed if you want to tie the two banks together or change which bank is connected to the house bank. Otherwise, it's never touched. When the motor is started, each alternator starts charging it's bank of batteries. When the motor is turned off, the banks are isolated so there is no danger of the starting battery being run down.
You might also notice the pulley is a bit larger than usual. We realized we weren't charging much at slow engine speeds, but were not turning the alternator at nearly the max rpm at the top engine speed. With a little calculation, we realized we could go to nearly a 10" pulley on the crankshaft, charge a lot more at slow speeds and still not over run the alternator at top engine speeds. We can now put nearly 100 amps into the batteries at just above an idle.