Save a life, start using a citation manager.
I also work as an editor, so I see a lot of dissertations (and you know, wrote my own and coached lots of people through theirs!) and if there is one thing I would universally recommend to everyone:
Invest the time and energy in a system for managing your citations - the earlier, the better.
Here are just a few of the reasons that I think including this in your workflow is well worth the effort:
Citation managers can act as a record of what you read, research, and plan to reference. Less time hunting for "where was that thing that I read about that thing?" which can save you tons of time.
Citation managers save the citation information so that you can easily switch the format for the citations (MLA, Chicago, APA, etc) on a dime which is a life saver if you're submitting to different journals.
Unlike web bookmarks or physical notebooks, you can sync citation libraries to work offline and in multiple locations - you always have the information you need.
You can set up citation managers to be shared across different groups - amazing for labs, authorship teams, or research teams!
Many citation libraries will also let you tag and organize references in collections, with notes, or with tags - searchable! Make a system that works for you, the same way you'd organize your bookshelves.
Some citation managers will also store your PDFs, and if they're scanned with OCR enabled, those documents also become searchable.
I love this article from the University of Chicago library about the pros and cons of various citation managers - it also has guides for getting started (although those are much more institution specific.) But in general, here are the parts of the workflow you'll want to think through when picking your software and working it into your reading routine:
How do you normally locate new work to read? Many citation managers have web browser extensions that allow you to save library records right into your library but if you work in an archive or with paper records, you will want to think through how you will keep track of those items and when you'll enter them.
When will you add your notes or tags? When you "process" a new document for reading, do you separate them into different categories? What tags/ways of searching for, or organizing information will best serve you in the future? When will you add that to the records?
At what point will you enter your references in the writing process? Before my citation manager, I'd do all my citations at the end - and end up being very frustrated because that is a slow, tedious process! Now, when I'm transferring into Word for final formatting/editing/sharing drafts, I add the citations using the processor integration, and then do a final check for formatting at the polishing stage.
Citation managers can feel, in the moment, like they're adding extra work. But imagine if you had all the notes for the readings you did as an undergrad, or in your MA, or during coursework at your fingertips. Imagine what it might feel like in 10 years to have all that information organized and accessible and you don't have to remember what you read for comps. Your brain is already holding a lot of information - let your citation manager help you keep track of what you're reading and referencing so you can clear up some much needed space for other things!