Serene,
I'll cover your second mention, getting rid of duplicate patients, here.
You are correct in that AC, and most EMR systems, do not actually delete a patient. Rather what they will do is mark a patient record has "hidden" so the particular record in question does not show up in search or reporting. This approach is made for compliance reasons. However, as you are finding, over time the duplicates can start to amass unless strict controls are placed over data entry.
Duplicate records are the bane of any database. They create lots of confusion and no one knows which record for a patient is really THE record.
Fortunately, I wrote a program some time ago that will de-duplicate an AC database. The program will merge chart records from one patient account to another then delete - actually delete - the duplicate record. There are some caveats to this program that you will need to be aware of. Hit me up if you would like to discuss some day.
While I do have this program available, I must stress there really is no substitute for training staff to ensure they do not enter a person into a system more than once. While things like duplication are expected to happen here and there, it should not reach a critical mass quickly.
James