This is what I do - it may reflect my 'unique' work flow .. but you may find it useful.
Typically EN is a note I make based on a document
Some times that document is an academic paper, sometimes it is a graphical representation of some data that I set up in (e.g.) 'Numbers'
I insert a line under the body of my note.
I use 'finder' to "get info" regarding the original document on my machine its easy to copy and paste ~/Documents/Work/Esoteric Academic Papers/Rare Thing.pdf ... six months later when I need to revisit the file; copy the path and use finder 'go to folder' and paste it ... you are there - read the original or modify it (but if the graph changes you need to copy and paste as an image into EN
Sometimes I just save the original pdf into EN (use a folder 'originals' or better a tag 'originals' and use "note link" again at the bottom of my personal note. Nowif you right click the pdf in EN and say open in Preview, annotations are nice and saved back to EN. Some times the original has a 'doi' or a reliable web address - similarly just paste the value.
I never save anything 'secret' in EN. My computers all back up and synchronise via SpiderOak.