What is it about your database that is not working and leads you into to want to convert internal groups into indexed groups?
See if this helps. I also suggest locating Greg Jones’ postings on using indexed groups, which provide a lot of precise and helpful advice.
Be aware that in most cases if you move indexed documents in the filesystem (say, from folder A to folder B) then your database will lose track of the documents – I believe Greg has a posting with advice on how to handle the move.