Frank,
We enter patients into AC as they come in to be seen. We then scan their paper chart and save that file as a PDF on a portable hard drive. The paper chart is then shredded. If any information is needed from the old chart, we access the portable drive and import it into AC. This has worked fairly well for us.
It was an adjustment going from paper to EHR. My favorite part is not having to look for the paper chart. The E-prescribing has been very helpful in that we hardly get any calls from the pharmacy anymore for clarifications.
You'll find this user board to be very helpful in that others have gone through what you are going through now. I usually turn to the user board first for any questions I have.
Best of luck!