Bert,
It only puts the allergies and medications in there if you have them in your note. It lists them under the Subjective part of the note.
If you use a blank note template with each follow-up then all you have to do is enter whatever you want in the Subjective in the HPI, Objective in the physical exam, and A/P in A/P. It works great for we dumb specialists who don't use the medications and allergies all the time and don't need that sent to our referring docs with every follow up.