If you are connecting the negatives to battery 2, connect the positives to battery 1.
You can do either, as long as the negative comes from one battery and the positive from the other.I see what you mean Paul. Probably better to connect the -ve bus to House Battery 1 and minimise serial connections on the -ve cables.
Are you planning to fit a battery monitor ?
In that case,the negative wiring isn't correct.There is a shunt and battery monitor already fitted on the house batteries only. Not sure how that one is wired (can't get to the boat until next week), but am considering replacing with a Victron Smart Shunt

Battery wiring is spot on. I would connect the emergency switch to the load terminals of the isolator switch, this has the added benefit of being able to isolate a dead/shorted battery and running everything from the good ones.Paul. Many thanks for your advice.
Here's v2 of my schematic showing the engine battery and alternator ground connected to the -ve bus, the shunt between the domestic batteries and
the -ve bus, and the domestic -ve and +ve from different batteries. I've also added the emergency parallel switch between the engine and domestic batteries.
View attachment 204438