Hello, I am trying to organize all my information. Does anyone label their ancestors, (like they do books in a library) and their sources?

For example: John Doe (Doe001), then put on his death certificate, military records, marriage record, and anything else that is his Doe001

You might check this article by Richard Pence on genealogical numbering systems. There are several:
http://www.saintclair.org/numbers/