So this might be a total noob question (which admittedly I am) I have a Motor, if I connect it to GND and the 5V output it runs. Ok so far. But if I connect it to GND and a pin set to OUTPUT and HIGH nothing happens. My multimeter reads 5V for both setups, so if 5V come to the motor one way or the other why does one work and one not?
That's probably caused by the motor's current consumption. The 5V pin can deliver much more current than the output pin in high state. If you want to switch the motor on/off by software, you need a "hardware driver" for the motor, in the simplest case a power transistor.