"From what I have read is that when you add a new deep you should put it on the top of the intial deep and then reverse them after the queen has started laying in the upper deep. Am I reading this correctly or am I misunderstanding."
dd, correct, when you add a new deep, set it on top, but there is no need to reverse the boxes in a new hive, the queen will move up and down. as others have said, reversing is normally done in the spring of the year. also, as pete mentioned, one must be careful not to reverse hives with brood in both boxes.
i am not one to reverse my hives in spring, unless the queen does not move down.