you keep with in the voltage limits for your card (check the hardware section of the web site).
For a very small motor via a transistor you can use Vin or V5v and both will work.
arduino is 3.3 or 5 volts, neither apply to a 9 volt wall wart ... why even include that when talking to a noob clearly stating what they have? cause applying 9 volts to the 5v pins will NOT work, unless your making a smoke generator.
to the op, use the power jack, it wont fry anything to have both external and USB plugged in