I wrote my doctoral thesis in Scrivener, using EndNote, and it worked brilliantly. The simplest way to enter a reference in Scrivener is to press Cmd-Y (to open EndNote), search for and select the relevant citation in EndNote, click (and hold) and drag it into Scrivener (and then release). While that is the simplest, the easiest way is to press Cmd-Y, select the reference(s) you want in EndNote, press Cmd-C (for copy), switch to Scrivener (using Cmd-Tab) and once the cursor is in the right place press Cmd-V (for paste). This will insert text surrounded by curly brackets {author, date, code}. When you later compile the document to Word, you can then convert these to properly formatted citations using the Academic style of your choice (I needed to use APA Style for my thesis).
Text like this*
will end up like this (using APA Style)
Note that, even if you were to write your entire paper/thesis/textbook in Word, you are better leaving the conversion to properly formatted citations until the very end. I strongly recommend avoiding CWYW, at least if you want to avoid headaches and complications. I have used CWYW in the past, but I was never going to let it close to my thesis.
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