Find what works for you.
It can be a binder and folder system if you prefer to work in paper only.
It can be a computer only system if you have a way to scan and organize all your information. This absolutely requires a fail proof backup system of all your information.
Most people will have a combination of computer and paper. Some things like family letters and pictures should be scanned, but also keep the originals as they are priceless.
Whatever your system, you should be able to both find and file away new information. Any information filed should be easily retrievable and the filing system should support that.
There is no one right way to do it. The best system is one that works for you and that your children or whoever inherits your research can easily pick up where you left off.