When running isolators, so folks put a relay/solenoid in to bridge the batteries temporarily when needed. This will usually be a push button switch somewhere on the dash and a Ford-type solenoid that connects the batteries when the button is pushed. This allows you to keep the batteries isolated, but still start the motor with the backup battery if you run down the main somehow...
You can do the same thing with a two-battery switch, but you have to remember to move it from "both" back to one battery to isolate them.
One advantage of diode isolators is they don't require any power when in use. All the relay and software controlled versions use a small amount of power all the time. That can be a problem for an unattended boat or one that is anchored for an extended period without power.
