Katy,
1. So you can see that this is one of those situations where you have a lot of choices. Like David, I do my procedures outside of the office so it is easiest to import them as pdf's to Imported Items. There is no right or wrong here.
2. You ask several questions here and the answer is a little complicated. After writing a note, you MUST sign it to permanently save it. (If your provider has not been signing the notes, then they have not been saved). You MAY add a cpt and diagnosis code, but you are not required to do so; the note will save without it.
Putting MU aside for the moment, if you are using a separate practice management program, you can leave the codes out and put them on a paper superbill that goes to your biller, (this is what we do) or you can put them into AC and they are accessible there. Others please correct me if I am wrong here...I think you can edit billing and diagnosis codes later, after signing the chart, if you choose to.
With regard to MU...it appears that for your CQM's and Menu items to count appropriately, in many cases you must have coded the diagnosis and E and M codes. Diagnosis must be correct (e.g. how can the program tell if you have gotten eye exams on your diabetics if you didn't code the diabetes). On the other hand, if the CQM items you use are not "diagnosis-specific" then you need not include the diagnosis codes at all. You do need to include a CPT. This need NOT match the cpt that you put on your paper superbill and submit for billing; you can just pick one when the provider signs off.
Sorry....MU makes this a bit confusing.
3. As the others say, AC does not allow this...except "section by section", cutting and pasting from Word to AC.