Unfortunately, upon trying to crank the engine, you discover both batteries are dead due to the battery switch having been left in the "all" position, draining both batteries dead. This is the dilemma many find themselves in when managing their batteries with a battery switch alone. Also, if the battery switch was left in the "1" position (main cranking battery) while the "#2" (aux. battery) was drained from use, how will it be recharged by the alternator if the battery switch is not moved to either the "2" or "all" position?

Another problem with utilizing a battery switch alone for dual battery systems is that when the boat is not in use for an extended period of time and the battery switch is left in the "all" position, the weaker of the two batteries can drain the the stronger one. An even more serious problem, which can ruin the alternator, is placing the battery switch to the "off" position while the boat's engine is running.

The simple fact is, dual battery switches alone leave too much to chance – like always having to remember when to switch to the proper setting for battery charging.

The simple solution to these common problems is to install a battery isolator (isolation diode or isolator or diode divider) to charge the batteries and utilize the battery switch for starter cranking (activating the starter cranking circuit only). When properly wired, this system will charge both batteries no matter what positions the battery switch is in. However, when using a battery isolator in conjunction with a battery switch, you merely leave the battery switch in the "1" position (for starter cranking battery) unless it becomes dead for cranking, then switch temporarily to #2 house battery for accessories (see wiring diagram below).

Furthermore, you will no longer risk blowing the alternator in the event the battery switch is inadvertently put in the "off " position while the engine is running. The reason being is that the charging circuit (alternator output circuit) is not wired to the battery switch, but to the battery isolator which distributes the charging current to both batteries through a diode (a one-way electrical valve).  

Instructions come with the battery isolator, along with various drawings as how to wire it with a battery switch. 

As aforementioned, since the isolator is an electrical one-way valve, the alternator current goes to both batteries without allowing current to backup through the isolator ─engine running or not. The center lug of the isolator is where the alternator output wire is attached and the terminals marked "1" and "2" on either side of the center lug is where you wire each battery for charging.

The isolator will also prevent batteries from draining in the event an internal alternator diode problem develops, which can cause a voltage draw on the batteries even with the ignition key in the off' position.

The auxiliary battery can be wired for the boat's main accessories/ignition feed wire and add-on items such an aerator and floodlights, etc.; while the other battery can be used exclusively for starter cranking only. Both battery positive terminals are wired to connect to the #1 and #2 isolator lugs according to the designated location on the isolator for charging purposes.

A boat's wiring diagram can aid in the specific location of the alternator charge wire (wire that charges the battery) and the accessories/ignition wire (wire that feeds the boat's fuse panel and accessories). Typically, these are located at the positive lug on the starter solenoid. After identifying the accessory/ignition feed wire, it should be disconnected and wired to the the #2 positive terminal (battery for accessories or house battery) with at least the same size gauge electrical wire. Then from the #1 isolator lug,  run another wire to the #1 positive battery terminal (battery for engine start/cranking). 

After identifying the alternator charge wire, it should be disconnected from the alt. and wired with at least the same size gauge electrical wire (#10 min.) to the center lug (alt. lug) on the isolator. The number #2 lug at the isolator is wired form the isolator to the #2 battery positive terminal house battery.

This isolator can be purchased for under $65.00 and should be a marine type only. The isolation diode is generally rated enough for the standard alternators on most boats, both inboards and outboards. Some systems have monitoring gauges for each battery which can be purchased at an additional charge.

An even better alternative for battery charging management is a battery integrator, more often used on outboard motors. Keep in mind that the integrator and isolator are not used together. You would use one or the other with a battery switch. The battery integrator device is more costly than the typical battery isolator, even though it serves a function similarly to that of a battery isolator or manual battery switch for charging the batteries. However, it offers significant advantages over both of these more traditional methods of battery bank isolation.

This device incorporates voltage sensing circuitry and a specialized solenoid/contactor to automatically integrate two separate battery banks whenever a charge voltage is being applied, then to isolate the banks when charging is not taking place. This allows charging multiple banks simultaneously from a single source (boats alternator/generator), yet permits selective discharge (electrical draw from accessories) of each dedicated bank.

Because the batteries are integrated by direct connection through the contactor, there is no voltage drop from the charging source to the batteries as with diode isolators, and because operation is automatic, there is no need for a manual battery switch to connect and disconnect the batteries before and after charging. However, a battery switch can be added if wired for cranking purposes ONLY as previously described when using and isolator. See diagram above illustrating the incorporation of a battery switch for cranking (starting) and an integrator for automatic charging of both batteries regardless of where the battery switch is set to.

The Battery Integrator features a heavy duty marine UL listed contactor and solid state circuitry. The housing is compact and hook-up is simple. The standard model accommodates two 12 volt battery banks. It is most notable to not use an external battery charger to charge the batteries unless all of the batteries are completely disconnected  from the boat's starting and charging system as this may damage the battery integrator circuitry. (charge batteries as a stand-alone battery, completely disconnected from all systems)

The unit may be wired to provide a "start assist" from the aux./house battery during engine cranking/starting if that battery bank has a higher charge than the reserve start/cranking bank battery. 

An optional contactor is available for integrating a third bank whenever the other two banks are being charged.