So I am integrating a 12v motor into my arduino circuit. I am using an ~10v power supply for the motor, and I need that power not to be diverted to the arduino+other components. How can I wire the motor to a transistor controlled by pwm while having the arduino powered by a separate 9v source? The trouble I am having right now is that the voltage I receive from the transistor is equivalent to the voltage I am supplying to the base (and I am not mixing up collector/base)
I'm using a standard TIP120 transistor
The trouble I am having right now is that the voltage I receive from the transistor is equivalent to the voltage I am supplying to the base
Sounds like you have wired it up as a common collector circuit and not a common emitter circuit.
See:-
http://www.thebox.myzen.co.uk/Workshop/Motors_1.html
Hi, The connections to the Tip120 are not what I consider "In Order" 
I realize that but I followed the circuitry diagram on the packaging so i think I got it right.
but I followed the circuitry diagram on the packaging so i think I got it right.
Are you just talking about the pinout?
Can you post a schematic of how you have wired the transistor, I still think you are using an emitter follower with the load connected between emitter and ground, this is not the way to drive your motor.