Watch out if you ever see a title like Book_Final_ReallyFinal_Updated2. At that point, it probably means the publishing process has become heavily dependent on your memory. Your manuscript will probably go through multiple rounds of corrections, authorial commentary, copyediting, proofreading, and layout checks. You shouldn’t have to make assumptions about which one is the most recent version.
First, you’ll want to gather up all the manuscript files in front of you. What you probably have is an initial draft, an initial draft with comments, an initial copyedited version, an initial proofread version, a final page proof (in PDF), as well as a couple of older files with vague titles. What makes the initial organization difficult here is not just the amount of files you have, but also the fact that each file may represent a specific decision type. One may contain word changes, another may contain style sheet changes, and another may contain layout-specific changes that should not be made to the manuscript.
Start with a simple organization process: name files based on stage and not adjectives. Words like “final,” “new,” and “updated” feel helpful in the moment, but become confusing after the second round of changes. You might choose a more explicit structure, including project title, date, and draft type (e.g. manuscript draft, copyedit, author review, proofread, or layout proof). The structure you choose doesn’t need to be complex, just consistent. File names that indicate the stage allow you to easily see which file is the editable version, which is the review version, and which is the proof version.
Keep files but separate the active file. Archive older versions and remove them from the main folder once you’ve established a working version in order to avoid losing potential valuable information but also keep the most recent version easy to find for you and anyone else who might access it. This way, if there is a question about a change that was made, you know what is likely the most relevant file to find that answer in. Or, if someone needs to jump into the work, the relevant file isn’t buried in a list of similarly-titled files.
Tracked changes and document comments need a similar system to help ensure they don’t get in the way. A draft full of open comments might be helpful as you begin to edit, but confusing during a proofreading process unless the reviewer is aware which comments are actually open questions, open notes, or items that should have been addressed by now. After an author review or change round, you will likely want to go through and see if any comments are open questions that need to be addressed, comments you need to address, or comments you have addressed that should now be moved into a style sheet or the actual work. One spelling choice shouldn’t be one comment in your third chapter; rather, you should note where in the style sheet that choice appears, so it can be replicated.
Practice with a handful of practice files. Name one file the current working manuscript, another the archived file, and a third the reference file (page proof or comments file). Then write a one-line note for the current working file to describe the draft’s state, any relevant history, and the next steps you’re hoping to take. You don’t want someone proofreading a draft that still needs to be copyedited or a page proof that should only have notes on the layout.
A robust system won’t make your manuscript perfect; but it should prevent unnecessary confusion. It’s working if you know what file is most recent without having to open each one and look, you’re keeping the earlier drafts but not having to sort through them, and you know when a particular version is most likely to be relevant for the current round. In the publishing world, this isn’t just extra busy work; it’s part of taking care of the book manuscript.