I would use the scanned copies as "working copies" and if you want to make binders print off your scans.
It may be tempting fate, but all of my originals (some 100+ years old) are in a metal box. Should there be a fire there is more chance of survival and all databases are backed up off-site (USB stick in desk drawer at work)
In answer to your question... I keep all docs in folder by type (birth, death etc) and then organised by surname alphabetically. This works for paper and electronic files
hope this helps