The factory switch thingies that are likely in your center-console require hooking loads to one of those three wiring harnesses you have. If you want to use them for things that are not powered by the van, you can certainly run relays off the outfitter switches for loads drawing from your (future) house batteries.
For ease of planning and math and such, prolly best to switch from 12VDC thinking with amps and amp-hours to watts and watt-hours. This helps make the planning easier when you'll be driving 5VDC, 12VDC, and 120VAC loads. You might even find that 24VDC or even 48VDC loads make sense for some things - and may make better sense for the house battery / storage as well.
So you're currently thinking ~5kWh of storage. Plenty for most usage - though mostly dependent on how you plan to replenish spent energy. If you plan to plug in to shore power every night, for example, then you could certainly get by with a lot less.
There is one element that sets the minimum, in most cases: the maximum acceptable draw (expressed in amps) from a given battery is typically 1.0C or less - with 0.5C typically being "better" for the longevity of the batteries - for charge and discharge. 1.0C for 400Ah is 400A. So, perfect world, you'd max load and charging at ~2.5kW rate. Plenty for a large draw - like an induction cooktop and/or microwave and/or hair-dryer or whatever. But if you drop down to 200Ah of batteries (@12VDC), the max 120VAC appliance (1800W max, typically, as you probably know) is already pushing the system a bit. Still viable (less than 1.0C) but not as healthy, long-term (as 0.5C would be).
From here on, it's all just personal preferences.
I prefer everything, "just works," the way things do at home: press a button and a light turns on/off; making eggs at the same time as toast - it should just work. To achieve this means leaning on the higher-end of the electronics - an inverter that CAN do 4kW or something like that. Generally, once you accommodate the largest loads, all the little stuff you mention (lights, fans, 12VDC outlets, 120VAC outlets, etc) are already accommodated.
Then you're back to the charging: 50A off CCP1 and 150A off CCP2 are the safest / easiest sources of 12VDC power. But you need equipment to use that for charging house batteries. This is where the option of running 24VDC or 48VDC house batteries comes in: you MUST use separate equipment to charge them anyway (even if they're 12VDC house batteries), so better to look to higher DC voltage for the efficiency it offers.