ADAFruite motor shield as Vin

jd2117:
The motor shield can supply 5v down to the Arduino but is this safe?

Not according to the circuit diagram I found on Github.
5volt coming from the Arduino is used to power the digital part/chips of the shield.
Current used should be low.

Motor power (12volt) can be connected to V-in (jumper), so Arduino's 5volt regulator can run off the same battery. Or (jumper removed) on USB power.
Leo..