Here are the first Five Rules of Genealogical Organization:
Rule 1: Every document has an owner
Rule 2: Every document needs to associated with its owner
Rule 3: Every document may have multiple owners
Rule 4: Keep and maintain, as much as possible, all original documents
Rule 5: It isn't organized until it is accessible
OK, so here is the next rule:
Rule 6: Paper is neither good nor evil
Here is a summary of how this all works up to this point.
It all starts with paper (or some paper substitute). Historically, at least since 1454 A.D., the most common way to transmit, copy or preserve information has been with paper. More recently, many genealogically significant documents have been preserved on microfilm. However, the Age of Microfilm is rapidly drawing to a close. For the most part the product of genealogical research was, and to some extent, continues to produce paper in some form or another. Let me describe how organizing your genealogical records proceeds by using a hypothetical situation.
We start with the average researcher (or AR) finding a document or other supporting record. This could be anything from a book to a certificate. In the past, those documents would pile up in the form of original paper records or copies. (I spent a small fortune on photocopies). In this hypothetical situation, I am going to focus on one, single record. In this case, I am going to use a birth certificate as an example.
So, the AR (average researcher) has a paper birth certificate. The first think she should do is reduce the certificate to a digital copy. She does this with a scanner or digital camera (cell phones work fine). She also enters the document in as a source in her genealogical database program. For this hypothetical, she is using one of the commercial programs that synchronize with the online FamilySearch.org Family Tree. She also attaches a digital copy of the birth certificate to her entry in her genealogy program. Now the program has a source citation to the birth certificate and an attached copy of the same document. She makes sure that this source and all the information gleaned from it are included in her records for each person mentioned. (I am not going into detail about the process of evaluating the source in this series). This is her first attached document, so it gets the first number in her numbering series. (I might suggest a number like "1" or something similar. Although, you could include a date such as 2015-08-12 (1) or whatever). Since this is an "original" of the certificate and not a photocopy, she adds the source citation to her document list/index/contents and puts the paper copy away for safe keeping (using proper archival methods) into a folder/box/file drawer/safe place.
She repeats this whole process for every document she finds. At the end of a few years, she has a huge file of documents, all numbered sequentially and an index to all the documents (hopefully kept on her computer). She also has a lot of people in her genealogy program and has been careful not to add people without citing a source. If she is smart, (which she is) she also uploads all her information to the Family Tree on FamilySearch.org and includes all the sources and digital copies of all the documents.
OK, now it is time to change the facts in the hypothetical situation. The AR in this second case has already got a huge pile of paper documents but no genealogical database program. He is faced with a much more difficult and time-consuming task. He needs to start entering his data into a genealogical database program. But as he does so, he needs to attach copies of all the stuff in his pile of paper to each appropriate individual. He is obviously helped if he had some semblance of organization to start out, but in many cases, he will be faced with documents that are owned by more than one person and he will have to go through the who procedure, just as if he were starting out from the beginning. He will have to look at each paper copy and verify that all the information and a source citation are attached digitally to each person mentioned in the document. He will also have to scan or digitally photo all the paper and make sure that the digital images and source citations are attached to the appropriate people in his genealogical database program.
As a side note at this point, I should point out that any paper organization you have developed that did not include a numbering system for the documents and somehow relating each document to each person mentioned in the document, is not going to a lot of help in getting the whole pile of paper organized. Color-coding and all that are not going to be much help but a numbering system can simply be added to the entries for each individual as you add them to the genealogical database program.
One last change to the hypothetical in this post. Let's suppose that the AR has both a pile of paper and thousands of names in a genealogical database program. He or she has just saved themselves a considerable amount of typing, but little else. If the entries in the computer program are extensive, any time saved in having already done the typing is usually lost in searching the list of sources to see if the source and a digital copy of the source have already been added to the program.
Don't get discouraged. There is no free lunch here. (See Heinlein, Robert A. The Moon Is a Harsh Mistress. New York: Putnam, 1966). It would have been wonderful if you and I had just had the insight to do something like this when we started, but now we have the programs, the paper and the task.