I have the motor shield on top of the ethernet shield on the Mega 2560, All purchased form adafruit.
1) Will stacking shields potentially cause any problems? And if so, how do I fix them.
That all depends which pins they use - you need to look at the pin usage of every shield. Some shields allow the pinout to be changed with jumpers which can help - however it is your responsibility to check for compatibility in pinouts - shields should have clear documentation about which pins they use.
2) How do I connect an external power supply to the motor shield? Will whatever supply I hook up, also be the voltage that the motors will receive? I am using four of these small 4.5-9V hobby motors (https://www.adafruit.com/products/711)
Do I just cut off the end of the 9V power supplies and hook them up? How do I determine which one is ground? (novice question, sorry)
I appreciate any insight
The motor shield should have screw terminals for its supply (yes that is for the motors), and terminals for the motor(s). The polarity of the supply terminals should be marked clearly (its very bad form if not) - ah yes, it has "+M" and "GND" marked.
What do you mean by "cut the end of the 9V power supplies", and what power supplies are you planning to use?