How best to power more than one Arduino board as part of a single project
You have a couple of easy options here: feed in an unregulated voltage, like the 12v, to the Arduino's Vin pin (on the Arduino headers), and let the Arduino regulate it, or feed in 5v to the 5v pin. In either case, of course, you should connect the ground pin to your PSU's ground rail. From the Arduino schematic, you can see that Vin is only used to feed the 5v regulator and the comparator for the USB/Vin switch, so if you power the Arduino over the 5v rail, you should not connect anything to the USB port.

Assuming you have a fairly stable and clean 5v source, feeding the 5v is the more efficient option.

You are correct that the Arduino is powered over USB only when no DC supply is present. This is implemented with a comparator, comparing half the voltage on the Vin pin to the 3.3v rail - so the switch will work correctly as long as power is supplied to Vin.