Props to you for seeking to resolve this now and not down the road. I'm a third year (nearly fourth year) PhD student and I've just started using BibTex with Org-ref and Emacs. I also sync references and .pdf's with Syncthing. In the past I tried Zotero, Mendeley, and a custom system where I created my own templates and stored entries in a MongoDB databse (this was a horrible idea), but all had some shortingcomings. Endnote was not an option for me as I don't use Microsoft products.
BibTex/Org-ref/Emacs/Syncthing has been a life-changer and is everything that I want in a reference management system. This specific setup, of course, requires that you use Emacs (which is an entire life path of its own). Emacs has been worth it to me but is definitely not for everyone. There may be similar setups that avoid Emacs.
John Kitchin (the creator/maintainer of org-ref) has created a helpful demonstration of org-ref that shows how powerful this setup can be.