I began by dividing my families into four groups under the surname of each grandparent and then subdividing each of those sections as needed. I color coded each of the four groups. Pocket folders are great for holding groups of files like vital records and correspondence.Military records, Land Records, Biographies and Genealogies are some more of the subtitles under each family.
Using the Librarians cataloging system is a good way to mark each document. Write on or attach to the document a title, date and place obtained, citation of book, name and address of any person or archive from which it was obtained and names of other families it pertains too.A log or separate sheet at the front of each section or file can be placed that says something like "see Gump file 123 for marriage record."It is a great idea to number each family group and use that too.
Lately I have begun using notebooks for my works in progress (WIP). I do not punch one of a kind documents but photocopies and printouts ofInternet research and the family groups work nicely.I used colored cardstock for dividers.That way everything is together and ready to travel when I am. I can refer back to them when I am in the library need to know piece of info from my files.I add one of those schoolkid zippered pockets in the notebook for carrying necessities like quarters, pencils, special library or membership cards and a power bar for an all day session.