No need to debate the shortcomings of such an arrangement
So you add a second battery .....you don't separate the domestic and engine circuits ... you fit a 1,2, both switch to simply select which battery to use and charge. See below.
From then onwards you can separate the domestic and engine systems to make the batteries dedicated to each add split charging etc etc making progressively more complex systems
Shouldn't be a mystery at all.
You should really trace your own wiring to understand what you have, as previously suggested.
Catalina 34 1986 #224 M25 engine 22# Rocna (NZ)