David,
I don't think this is as onerous as you are picturing it. As the provider signs each note, AC asks you for a cpt and a diagnosis code. Since you don't use AC for billing (as I don't) you may have clicked the box to turn off this request. Turn it back on, and simply have the provider pick a cpt as they sign the note. It need not even be the same one you actually use for billing. I believe that is all you need to do to get the wizard to count the encounter. Others can correct me if I am wrong about this.
The process described above by Wendell is only needed if you want to go back retrospectively and add a cpt to previously signed notes.
