Keep all files in your computer in separate folders, also. This is one of the easiest things to do and saves more time. That I can tell you. Always back up your business files from your computer to some kind of removable storage. File folders are one of the greatest inventions of all time.
Filing is one of the worst jobs ever invented.
Make it easy on yourself by filing everything as soon as you get it. This calls for lots of file folders and hanging file folders. Keep a tickler file that has a section for each day of the month. Put papers into the day that it needs to be taken care of. Keep office supplies all in one place and close by.