I assume you are after an engine battery and house battery. Connect
both batt negatives to common ground. Connect domestic battery pos to
a on off batt switch - do not bother with a 1 2 all switch. Connect
dom bat pos to eng bat pos via a relay - Curtis/Albright - controlled
by something like a Smartbank - www.smartgauge .co.uk Connect
alternator pos to domestic batt pos or batt side of batt switch -
replace weedy std alt wiring with something more beefy. Can leave alt
neg connected to common ground. Have a suitable feed from live side
of batt switch to supply "always on" items - bilge pump, alarm etc
etc.
Smartbank will control when relay operates - charging engine battery
when engine is running and then disconnecting engine battery. Smart
bank can also be used to parallel batteries for emergency starting
using RJ45 cable and push switch.