Doing what Omatako suggests...switching your perko switch with the engine and alternator running will result in burned out diodes and a major alternator repair. Don't try it. I don't know what setup he has that allows him to do this but it is not the "standard" USA type alternator 4 position switch.
Omatako...you said...I've been told that if one battery is at say 13.2 volts and the other at 11.9v and you set the switch to "Both" the regulator will sense the higher voltage and will go to float charge mode and the flatter battery will stay flatter...
Actually once your batteries are paralleled by the "both" position on the switch, the charger only "sees" the combined voltage and (assuming identical batteries) this would be approx. 12.5 volts and would charge both until they reached 13.2. This is less efficient than simply charging the flat battery as you can bulk charge it more quickly when it is isolated.
Barry...running the engine with the battery switch in the both position is fine for a day sail...but should be avoided on a cruise. If while running, the alternator fails...your instruments will run down both batteries leaving you no way to se-start the engine once you've realized the problem exists. Don't ask me how I know this!