Khaled,
When I think of breaking down the process of handling an endo report, there are (at least) four components: creating the report, "filing" it in AC, sending copies to referring docs (and perhaps patients), and billing.
I do procedures at three places, and the process is a bit different for each. You have gotten suggestions here that illustrate some of these variations (e.g., dictation vs. templates for report generation).
Your specific question was about billing, and again, there are several options. First question I have is "who does the coding"? Assuming you do it, and that you want your staff to generate the bill, then you need to communicate that information to them. You can include it (cpt and icd9) at the end of the report. I like my reports (which are really being generated for the referring docs) to be as readable and free from "gibberish" as possible, so I don't put the codes there, but if it works for you, then go ahead. After I dictate (or type the report) I go into my schedule and type what I did into the comment section. That takes just a few seconds of my time. At the end of the day, your staff can do what Apricot describes to create the bill (they don't have to create an addendum).
Would that work?