For any citation workflow with Scrivener, you do not use CWYW, nor do you need it. You use plain text citation tags (TC), unique IDs that are simply more robust and less prone to bugs. I’ve had to deal with several document corruptions from students or colleagues using CWYW over the years, and my recommendation is, even if you use only Word + Endnote, turn it off. But that is my own personal advice. The choice nevertheless is clear, if you want to benefit from Scrivener’s superior writing system, you use plain text temporary citations.
Here are some instructions for the TC workflow for Endnote, though note I use macOS so there may be some subtle differences for Windows: