The first four of this series present (what I hope are) InDesign best practices for working with certain types of documents, which I developed over the past couple of decades of working with InDesign (and before that, Xerox Ventura Publisher). I use InDesign not as my "day" (but often night) job – that's being an academic emergency physician and medical school professor, with a subspecialty of the medical aspects of mountain and cave rescue.
I started using InDesign for handouts for classes I teach. You can see examples of the PDFs I have produced using InDesign at http://www.conovers.org/ftp/ including, for just a couple of examples:
http://www.conovers.org/ftp/Ticks.pdf and
http://www.conovers.org/ftp/Poison-Ivy.pdf.
As you will note from those two samples, there are lots of references, more so in the ticks handout. Managing such lists of references, in the approved medical manner of using superscripted numbers in the text in order of appearance in the main text, can be a royal pain. The application EndNote has justifiably become very popular for managing references and taking care of this for you:
I can download a PDF, and drag and drop it into EndNote. The PDF metadata creates a bibliographic record in EndNote. For references I can find in Google Scholar, without a PDF, I can click "Cite" and the biliographic record gets imported into EndNote. I can group the records by topic, or search them, making it easy to find the ones I want to cite in my document.
And, if I'm working in Microsoft Word, I can select a bibliographic record in EndNote, up at the top of the screen, pick a citation standard such as that for the New England Journal of Medicine (NEJM), click a button, and the superscripted number appears in my text in Word, and the NEJM-formatted reference appears in the bibliography at the end of that document with that number attached to it. Slick.
But. Have you every tried to do graphic layout in Word? It is enough to make you want to punch your computer. Don't, it's not the computer, it's Word. Don't get me wrong. Having used word processors back to CP/M and DOS days, Word is really quite good at its primary job. Especially because I use AutoHotKey to remap keys to be roughly similar to the old WordStar control keys (see https://en.wikipedia.org/wiki/WordStar#Interface). That way I can touch-type many commands without my fingers having to leave the keyboard. I could do something similar directly in Word, but by using AutoHotKey I can use similar keystrokes in all sorts of other programs, including here in my browser, and in my programming editor, UltraEdit (actually UEStudio which has a spellchecker and other features as well as all of the context hinting of UltraEdit for actual programming, including writing AutoHotKey macros, though you have to manually add the context hinting for AutoHotKey). For more about usability and switching input modes, see https://ed-informatics.org/2010/02/11/medical-computing-10/. Yes, another medical subspeciality of mine is informatics, particularly usability and UX (overall User eXperience).
As I said, Word sucks at graphic layout; its attempts to make things easier for you actually makes things harder, but with integration with EndNote, it makes writing academic papers with references a breeze. (I remember, not at all fondly, the days when I had to manually format every reference.)
Unfortunately, EndNote has no similar integration into InDesign.
So, you just need to write the document in Word, then Place the Word document in InDesign, and do your graphic layout in InDesign. But. There is this "little" problem with Word import into InDesign. Unless you create and use Word character styles for bold, italics and superscript instead of the builtin ways to do these things, InDesign will change text to (for example), italics, but not change it back out of italics when Word changes back to italics. Then you end up with an InDesign file that looks like:
If you manually change every instance of italics or bold in the Word document to a character style (is there some easy way to do this? I don't know of one), you still have a problem. Note that EndNote automatically applies superscript after every superscripted reference in the text, and the text stays superscripted until something changes it back. As far as I know, there is no way to fix this by assigning a character style instead of Word's internal superscript to the EndNote citations.
So, this is more a plea for best practices than the first four topics in this series, which were suggestions for best practices you should (maybe) emulate.
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