Thanks guys. And I feel dumb for asking, but its safe to say the starboard battery with Yamaha labelled positive cable is the start battery correct? That battery appears to have everything hooked up to it - bilge switches, windlass, etc. My port battery only has an 6ga pos and neg, and small ground connected directly to the fuel tank.
Technically, your system doesn’t have a Start battery yet. It’s just got two batteries, either one of which could be selected for cranking purposes by the original 1-2-BOTH-OFF switch. So you can designate whichever one you like as the Start battery to connect to the appropriate input terminal on the BEP cluster.
That said, there are a couple things to take into consideration here. I’m curious as to why there’s a pos Yamaha cable going directly to the battery? The pos cable going to the starter and alternator on the motor should be hooked up to the output terminal on your existing switch. Only possibility I can think of is if you have an auxiliary charging cable coming from the alternator. Probably worth tracing out where that one goes.
Regarding everything else: the only things that should be hooked directly to the battery terminals are the pos cable going to the switch, the neg cable going to the main negative bus, pos and neg leads from a battery charger (if installed), and a fused wire leading to the bilge pump float switch (possibly more than one, if you have multiple float switches installed). Everything else should get power from a source of power downstream of the main battery switch and main/secondary breakers, and should return to either the main negative bus or a negative busbar attached to the main bus. The bilge pump fused power should be hooked up to the house battery: it usually has more capacity than the cranking battery, and will therefore run the pump for longer before dying; and it preserves the ability to crank the motor regardless of whether the pump has run down the battery.
Possible exception to the above: the windlass. I advise that the windlass should be powered from the start battery circuit. The reason for this is that you’re unlikely to be using the windlass if the engine isn’t already running, and providing alternator power. With a BEP switch installed, if the VSR is open (as it would likely be shortly after cranking the motor, until the start battery charge is replenished by the alternator) the start circuit is receiving all the current from the alternator. Thus there will be more power available to run the windlass. As far as connecting the windlass, there are a couple options: 1) Connect the windlass directly to the Start battery terminal, running the lead through a dedicated cutoff switch and a breaker. This allows you to independently de-energize the windlass circuit with the switch, but requires another connection at the battery terminal which may not fit nicely under cable boots or other insulators. 2) Connect the windlass directly to the battery terminal and use a trippable breaker (such as a Blue Sea 285) that can be manually opened as circuit protection. Same issue with the extra connection at the battery, but the trippable breaker allows you to manually open it if needed, essentially acting as a switch, which allows you to eliminate the separate cutout switch. 3) Connect the windlass to the output of the Start battery switch on the BEP cluster, and use a trippable breaker for circuit protection. This was my solution; it allows me to minimize connections at the battery terminals, and all electrical components are deenergized with just the switches at the BEP cluster; I can also isolate just the windlass circuit for maintenance or malfunction by manually opening the breaker.