On the corollary and unmentioned topic of management of power distribution with two batteries available and for management of the re-charging of the two batteries, the best arrangement will provide for isolation of the two batteries and their loads from each other, and for isolation of the re-charging of the two batteries from each other.
Altering the power distribution wiring so that loads are isolated to one battery or the other is straightforward, and I will not attempt to describe the method here.
Re-charging each of two batteries in isolation is best accomplished if the charging source, typically an outboard engine, can provide two isolated battery charging outputs. Many engines have that feature.
If isolated charging outputs are not available from the outboard engine, the next-best option is to employ an automatically-operated battery combiner switch. These devices are generally sold under the designation of ACR (automatic combiner switch) or VSR (voltage sensitive relay). Such an arrangement typically lets the engine charge its attached cranking battery in isolation until the engine cranking battery terminal voltage rises to a threshold level which is indicative of being at a state of full charge or near full charge. When that voltage threshold is reached, the automatic combiner switch is activated, and the second battery is placed in parallel with the engine cranking battery. This action also places all the loads in parallel, ending the isolation of the loads when the two batteries are not in parallel. The charging current from the engine then will begin to re-charge the second battery while wired in parallel with the first battery.
Of course, such switching could be accomplished without the automated feature by the operator just manually operating a switch that placed the two batteries in parallel at the appropriate moments and separated them again when appropriate. The automated feature is generally based on sensing the voltage of the engine cranking battery.
If the second battery is at a very low state of charge, when it is added in parallel with the primary battery the effect of that combining may cause the terminal voltage of the primary battery to drop below the threshold voltage for combining. When the combing has been ended, the terminal voltage of the primary battery again rises, causing the combing to reoccur. This behavior creates an oscillation in the combined or not-combined state. The better devices use a second threshold voltage to be the decision point for uncombing. In a control circuit this behavior is known as hysteresis, and is an important consideration in creating useful control. In choosing an ACR or VSR, be certain the devices incorporates hysteresis in the combine-threshold and the un-combine threshold voltages.
Some products that provide this function also include more features, such as feature that restores complete isolation of the two batteries and their loads during engine cranking. This avoids creating problems with electronic loads from battery voltage sag during engine cranking.
These products are well-known and are described in detail by their manufacturers, so I will not attempt to describe them further here.
For some prior discussion on this topic, read these earlier articles published some time ago:
DUAL CIRCUIT BATTERY SWITCHEShttp://continuouswave.com/forum/viewtopic.php?f=9&t=2627AUXILIARY BATTERY CHARGING KIT FOR E-TEChttp://continuouswave.com/ubb/Forum6/HTML/002758.htmlBLUE SEA SYSTEMS Automatic Combiner Relayhttp://continuouswave.com/forum/viewtopic.php?f=9&t=912