Being pack leader or not will not alter marking. Dogs will mark even if they are the lowest in the pack. In fact, if this little dog is a dominant boy he will simply mark over the top of your marking.
zen - unless you catch him in the act he won't understand why you are telling him he is a bad dog. He will only associate your current action with his current action. Dogs have intelligence but not in such a way that they can think back to what they did and understand that the gobbly gook coming out of their humans mouth in a deep undertone is related to something that happened some time back. They only live for the here and now.