Issues, and more info need.
Need more info: is there also a house battery, and if so, how is it wired?Assuming there is not, and this is the only battery system on board, there is a serious problem with this topology. First, I don't know what "most boats" have, but wiring the alternator to the common terminal is a mistake, unless the battery selector switch is of the special type that has an alternator field disconnect switch. Without it, if you select "OFF" while the engine is running, you will destroy the alternator rectifying diodes.Without addition equipment, it would be best to connect the alternator output to one of the batteries, say batt. 1; connect the load, starter or all loads, to "COMMON;" and then wire batteries one and two to switch terminals "ONE" and "TWO."In operation one would start the engine by selecting one or two or both, select both while charging; and select one or two or off when the engine is off, depending on whether you are running loads. "BOTH" would be used if the batteries are a matched pair of house batteries, meaning same type, age, and history. If you already have the house battery issue solved and simply want to add a back-up starting battery, I recommend a battery isolator, or automatic charging relay, and then the selector switch you have to connect the batteries to the load (starter plus engine electrics). This way you could always leave the switch set to "ONE" and both batteries would charge when the engine runs. Bear in mind the isolator will introduce a voltage drop that may result in poor charging unless compensated for. Also, if the boat has a single alternator and it is also used to pump up a big house battery via an external charging regulator, you may damage the starting batteries over the long term; however, the isolator might actually help in this case, dropping the usual acceptance mode charging voltage of 14.2 to 14.4 (temperature dependent) that the starting batts would see down by a 1/2 volt or more, pretty close to the usual float level of 13.8, which most batts can stand forever. This all assumes wet cells. Levels are different for AGM and gelled cells. An echo charger, as someone previously suggested, would work well here, too, 'though you'd still need to get it connected to both starting batts somehow. More information about your boat's electrical system, including any other batteries, would help the analysis.