Richyo, great to hear from you. The short answer to your question about Endnote is: Endnote is designed to be a home for academic references, which helps not only with having a structured source of information on articles, books, reports, etc., but also allows you to insert those references and bibliographies much easier than doing it manually (and it accommodates a variety of citation styles and allows your to adjust them to fit the journal).
DEVONthink doesn’t have anything close to this, so inevitably your academic references will not be stored in as structured of a format and will not be able to be automatically inserted into your work.
If you are pursuing an academic career or even a career that involves a lot of writing, I strongly encourage you learn how citation managers like Endnote work as early in your career as possible as it will ultimately save you enormous amounts of time.
The brilliance of Devonthink’s ability to index is that you can index your Endnote library and get the benefits of both a structured source of references AND Devonthink’s amazing search abilities, PDF editing, tagging, etc.
I wrote a post previously that you might find helpful: Tools of the Trade: How to Automatically Import and Organize Your PDFs In Your Digital Library.
Hope this helps.
Austin Kocher