Hi Paul. These are two types of programs. When you are setting up an "Email Program" you use the Smart List in the Audeince Tile. This acts the same as when you have a regular program which contains a smart campaign with a flow step to send out an email. These two, in effect, are identical, they just have different presentations and some underlying features.
There is IN ADDITION, a Smart List which you can add into a program as a local asset. That Smart List is going to tell you real time information about your database. Think of it like asking a question, "Tell me all the people who visited page X, or show me all the people who come from Company Y."
So ... These are all Smart Lists. They define an audience for you. Whether you're using a Smart List as a standalone local asset, or as the beginning of a smart campaign or within the slick UI of an Email Program. They all have the same basic function.