There are many ways to do a layout for multi-engine boats, here is one simple way to do it using remote switches. This is a greatly simplified drawing that only shows positive wires and omits circuit protection. The boat has two engines, each with their own starting battery, and a large house battery. Remote battery switches are used so that the switches can be as near the batteries as possible (as required by ABYC) while also being accessible (also per ABYC). These two requirements are pretty much mutually exclusive on a larger boat unless remote switches are used. The switches shown have manual lockouts for servicing. Each load has a switch to its respective battery, and the three battery banks are liked together using Automatic Charge Relays (ACR's) So when any engine is running and charging its dedicated start battery the ACR's will combine and send the charge to all the batteries. As soon as the engine is stopped or the charge source goes away the ACR's will separate and each battery will be on its own. In the event that a start battery is a bit flat the ACR's can be forced into a manual override combined position to allow starting from all the batteries combined.
In this system charging is allowed between batteries even if the load of the battery is switched off. So for example if the port engine were disabled and turned off for some reason its battery would still get charged from the starboard engine.
In the layout shown here (for a 12 volt boat) the remote switches are Blue Sea Systems 7700 ML-Solenoids rated at 500 Amps and the ACR's are Blue Sea Systems 7622 ML-ACR Each switch or ACR comes with a remote switch, and for this layout you would end up with a total of five remote switches. Each remote switch has an indicator light to show the status of its operation.and the ON-OFF switches have lockouts so you cant accidentally turn one off and fry an alternator. Here is what a set of three switches would look like if mounted on a 360-Series panel:
You would probably end up putting the three battery switches in a row and then on a second panel the two ACR's and a blank. A blank panel to mount three switches is available and is part number 1520
If you are designing a new custom 360-Series panel these switches can be easily accommodated and below is just an example of what it might look like: