My workflow is that I tend to gather PDFs directly from journals, but in previous versions of endnote (I have X for windows) I had to manually input the citation info. I’d suggested this a few years back, but does X3 (mac or windows) have the ability to accept a PDF into a library then auto-extract citation info?
An alternative citation manager that I won’t mention by name, and which I’m not using because I prefer endnote, would parse the PDF for the DOI number and then lookup based on that (though this method failed probably 10% of the time for me–certain journals’ PDFs didn’t have a “properly” formatted DOI number and auto import would fail for those).