1. Create a note and name it in your usual citation style. e.g. "Connell 1964". Use a template where you include the DOI at the top. Here is an example
2. Scroll down to the bottom of the note and use the "Inset Attachment" command. (Hit ctrl/⌘ + P and type in "Insert Attachment")
Now select the file you have downloaded to embed it directly into the note.
Pro Tip: Assign a Hotkey to "Insert Attachment" to use it instantly.