I have just installed Office 365 on my Macbook and then installed Endnote X7.3.1 and have found that Endnote does not show up in the Word menu. Looking in at the Endnote customizer I found that Endnote doesnt seem to recognise Word 2016 because it isnt installed in an Office folder the way Office 2011 was. How do I get everything working together?
Unfortunately there are compatibility issues between the two - refer to this thread and the knowledge base article cited.
Have you looked at this one? http://endnote.com/kb/136020
I am very dissapointed in the lackadaisical approach that Thomson Reuters has taken with this. I enjoy Endnote and have used it for many years. However, the lack of support coupled with the lack of communication to their customer base is surprising.
It is time to switch to Mendeley.