I have been saving all my records to the computer, scanned images (birth,death,marriage certs), downloads of census, LDS pages coppied into a Word document etc.
I have directories starting with a Family Line, Then surname. The records are named thus Surname First name byear record type. Record type might be 1851 census, Birth Certificate, wedding Picture etc.
I have an external backup drive and I also share the data to my laptop so when I go out I have the upto date data.
There is a family tree program called Family Historian that allows hyper links to documents which can be inserted into the Source area. I have suggested this to Genealogy twice but they don't seem interested.