hay welcome, anyway yeah since the pot is connected only to the arduino, it won't be affected by the motor shield, how ever i would recommend to you to find a higher unregulated supply of between 7 to 12 if you powering the arduino. this is due to the on board voltage regulator, there must at least have a minimum of 2 volt higher then the regulated output of 5 V. however if you supply the board with 5 volt, arduino probably only get something less then 5v. however this does not meat that the board cant function, just the operation is not optimal. anyway about the motor shield yes it is suppose to be hot, this is due to the amount of current flowing thru the I298 ic. it is wise if you could make a heat sink for the ic of like you suggest putting a fan might help too. or maybe both is better.