EndNote X9 allows you to collect, organize and store citations on your desktop and sync with your cloud account to keep your library current.
You can comment on pdfs and search those comments later
Getting Started Guides
5-6 Minute Overviews for Mac and Windows
The library recommends searching the actual databases and NOT using the EndNote interface.
Short Course Webinar Recording (25 min)
Although this is for Windows computers, Macs should function very similarly.