With the inactive charts we scanned them whole. We have recently started on the active charts and are separating them into administrative, written notes, labs & xrays, consults and hospital, immunizations and schools PEs sections, which does take more time both to separate and scan.
We use a fujitsu M3093 scanner I picked up at ebay. It will do 25 sheets double or 36 sheets single sided. The scanning is the easy part.
It does take a while to get all the scanning done.