I have three identical group 27 deep cycle batteries on our boat, but that's because we anchor out a lot, often for week or more.
It's a single engine boat. Battery 1 is used as the starter battery. Batteries 2 and 3 are house batteries. The boat has a two bank (two battery) three stage AC powered smart charger that is used at the marina. I wired the charger so I can charge/maintain batteries 1 and 2 together, or battery 3 separately.
At the marina and under shore power, all batteries are switched OFF, but auto bilge pumps are hot wired directly to battery 2. The charger is left on, and directly wired to the positive battery terminals.
Under power, battery 1 and either 2 or 3 are switched on.
At anchor, battery 1 is alway switched off and either 2 or 3 is switched on. The boat is designed to get by with very low battery power (usually less than 30 amp/hrs per day). Batteries are recharged at anchor with thin film solar panels. One house battery is used for one day, then shut off and recharged the next day.
vv: How many engines on your boat?