Why you only want two battery banks on board:
Minimizing the number of battery banks maximizes battery life. Most reasonably sized boats only need two battery banks: One bank to start the engine, the other to power all other loads on board. While an emergency switch to combine them should exist (to use your house bank help start the engine if the engine bank is down), the two banks and circuits should be completely separate. There are several benefits:
Your starter bank is always full:
While starting engines requires a lot of power, the burst is relatively short. Thus the net drain on your starter battery is small and even a short commute out of the harbor will pretty much replenish the charge that had been used to start the engine. If you accidentally run the house bank flat, you can still start the engine and recharge the house bank.
Most external regulators have outputs that allow you to drive a solenoid that combines the two battery banks during charging and disconnects them afterwards. You can also use battery combiners to achieve the same effect. I would stay away from diode systems because of the voltage losses associated with them. A more elaborate, battery life maximizing solution can be found in the isolator/eliminator manufactured by Ample Power that treats your starter bank as a completely separate bank and charges it accordingly.
Your electronics will behave better:
When the starter and the house banks are completely separate your electronics and other circuits will not experience the voltage transients that starting an engine produces. For example, our electronics would drop out every once in a while during engine starts, suggesting that the voltage levels on board dropped below the 10V threshold that the instrument and GPS package could still run on.
Battery banks last longer, provide more charge:
Less depth of discharge and lower rate of discharge (i.e. battery bank Amp-hour capacity vs. discharge) will make your batteries last longer in terms of cycle life and in terms providing energy. In his excellent tome on boat maintenance, the "Boatowners Mechanical and Electrical Manual", author Nigel Calder provides convincing arguments why a large bank of cells will always outperform the constituent batteries by themselves. Ample Power and other manufacturers of charging systems come to the same conclusion.
Not only will a collective bank be affected less by Peukerts Effect (the smaller the rate of discharge, the more juice you can extract from a battery or battery bank) but the depth of discharge for a large bank will be less than if a constituent battery had to carry the load alone. Depth-of-Discharge (DOD) is one of the most important variables that determines the life of your batteries. The faster, deeper you charge/discharge lead acid batteries, the shorter their life.
Some things to keep in mind:
The only caveat to large banks of batteries is proper internal fusing. If a cell shorts out in a battery, the battery voltage will drop approximately 2 Volts. All batteries in the bank will start discharging into the shorted battery, unless fuses take the bad battery out of the circuit. Thus, battery banks need to be fused internally as well as externally.
Remember, your entire electrical system has to meet all requirements: Wires, fuses, chargers, batteries, alternators, etc. The ABYC requirements are a good first step in that direction and guides such as Mr. Calders are easy to understand. More fusing and wiring information can be found at Blue Sea Systems.
Onwards then to some Cost Comparions!