My first suggestion is, do try to get deepcycle batteries insted of car batteries. You will be much happier with them.
Now as for voltage, if I understood properly you ran a set of lines for both voltages?
If so consider this, make all your lighting and other such hardwired things 12 volt, that way you may have the convenience of lights without needing the inverter to run them... you will find this particularly nice should your inverter ever fail!
Then as far as convenience receptacles use the 120 volt inverter output to feed those, this gives the advantage of using standard appliances and the inverter may be shut down entirely when no accessories are in use. You would of course want a few 12 volt convenience outlets for things that require power 24/7, like cordless phones or answering machines... LCD TV/Monitor perhaps, battery chargers for cordless tools etc.. your cell phone's 12 volt charger or your laptop charger. But if someone comes to your house they will be greeted with a familiar 120 volt receptacle that is compatible with their things.
The most recent system I am installing I'm doing in exactly this way, except I also have 24 volt available at the receptacle as well for heavier loads like 24 volt refrigeration.
I was able to use one type of duplex receptacle for both of my DC voltages... so it's almost fool proof... unless the non-fool wires it wrong... but that can happen with anything at any voltage, just be attentive to the work at hand and those issues are avoidable.
On my 120 volt side I have a 1KW inverter that feeds all the "standard" receptacles.
But surprisingly even with construction going on it remains off most of the time.
As for switching of DC lights just use a good quality snap switch (do not use quiet switches, they don't open fast enough), they will switch DC lighting loads up to 5 amperes safely which at 12 volts is a fair amount of light if using compact fluorescent. Although you may want to add an electrolytic capacitor across the switch's terminals to control arching if your load is close to that 5 amp range.
For most of your general lighting use 12 volt CF's, a 13 - 15 watt spring/twist style will give as much light as a 60 watt incandescent and one or two in a room provides good evening light levels. For task lighting.. like a desk lamp or under counter lights, LED's work well.. but if you need BRIGHT light use a fluorescent.
I particularly like the LED halogen replacement/imitation bulbs for spotlighting artwork and paintings.. but you may want a UV filtering lens to protect your artistic investment.
Hope the new mill comes out well!
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crashK6