What is the best way to tap 12v from a 6x6v battery array for intermittent loads?
I don't like tapping only 2 of the batteries, since prolonged usage will imbalance the batteries and possibly require individual charging.

Unlikely. The power draw from the accessories is probably small as compared to the engine draw.

Can I wire 3 12v circuits in parallel from the 6 batteries for an always active supply.

Not if you still need 36V for the engine as well.

or would it be better to add a separate switched 36v circuit and a buck converter to get 12v?

I assume you want to use the 36V from the engine supply. You can convert this down to 12V but that seems overkill and will also create some non-trivial losses (and cost)
If you are really worried about asymmetric use, simply switch the accessories to a different battery pair every 100 hours or so. If the accessories share a common ground with the engine, than you can just shuffle the batteries instead.