Flashpants, On my 200 R-25, all four batteries are in parallel "most" of the time - independent of the switch settings.
My boat was factory wired (and correctly reflects the wiring diagram) to automatically connect with two ACR (Automatic Charge Relays): 1) house and thruster + 2) house and starter. This way, the single power source from the engine alternator will charge all three banks - as will the solar cells that are, on my R-25, connected only to the house.
The factory battery charger is connected to all three batteries - each isolated with a diode that lets the respective battery charge without permitting draining should one battery get low.
I am unable to determine what the "house" and "engine" and "emergency" switch do on my R-25 - disconnecting or shorting them has no apparent effect, but with the Automatic Charge Relay (ACR) in place, there should be no effect.
All is good normally. But, if the STARTER battery is weak, for some reason, the ACR will automatically disconnect it from the House battery preserve what power you have. When mine aged, everything worked until I shut down overnight. At that point, the STARTER battery drained from age and the HOUSE battery drained from load. The "emergency" switch does nothing on my boat, but bridging the ACR immediately started the engine. You need only about 12 GA wire for the bridge - that is enough to turn on the ACR and transfer power to start the engine.
West Marine sells a perfect switch for this: COLE HERSEE M-608 Moisture-Sealed Switch
https://www.westmarine.com/buy/cole-her ... cordNum=19
Wire this across the two heavy terminals on the ACR - it will cause the ACR to turn on so you can start the engine. Just push the button for 10 seconds or so - assuming your solar cells are working - and the STARTER will come back online.