Separate battery banks should be installed for engine starting and general 'domestic' use. When installed correctly, this prevents the domestic usage from flattening the engine starter, or cranking, battery. Further separate battery bank(s) may be justified if an 240v inverter or, for those who can't manage without them, a bow thruster is envisaged.
 

We must avoid the cranking battery from being drained by the other battery banks, whilst the engine is not running.  It used to be the norm for a simple relay to do this job.  When charging systems were fairly simple with low powered alternators, that may have been satisfactory - but not today.  If a battery bank, for any reason fails, a modern alternator may attempt to charge the failed bank using high amperages - which may dangerously overload the relay. In our view the best option is a quality splitting diode system (although there are those who still like the old fashioned rotary switch). 
 

Each battery bank should have an appropriate amp / hour capacity to suit it's particular task and the lifestyle of the boat's occupants . For example, on 'Willow' with a relatively large engine and high domestic usage we have a 90amp/hr crank battery; 330amp/hr domestic battery bank; and 330amp/hr inverter battery bank.
 

The alternator should be of a size, in charging capability, to suit the total amp/hr capacities of the battery banks it is being asked to charge.  'Willow' has a 90amp alternator which works efficiently enough - but we would prefer a 120amp version were we not constrained by the physical size of the unit.  If your engine can be fitted with two alternators - all the better.
 

BUT a suitably sized alternator with adequate battery bank amperage capacity will be of little use if the alternator's regulator is designed merely for automotive use. For most of us an advanced alternator regulator (often called a battery management system) should be installed to override the automotive regulator and thus obtain best advantage of the alternators rated output. At the same time these advanced units have built in provision to protect batteries from over charging.  If there are to be warranty issues with fitting such a system to standard alternators, newer technology is now available to achieve the same result whilst avoiding the warranty problems.