There are 4 ways to add references to your EndNote library:
Search within EndNote
Export from databases
Import a text file
You can organize your EndNote library using groups. To create a group, go to Groups --> Create Group. Name it, and then drag and drop references into it.
There are other types of groups:
You can also create a Group Set, and file groups themselves by dragging and dropping
When you add references, you're just getting the citation information. However, you can also attach PDFs, which can then be annotated inside EndNote.
Have EndNote do the work
Have a PDF (or folder of PDFs...) and just want to quickly import it into EndNote as a reference?
You can easily annotate PDFs in EndNote. Double click any reference that has an attached PDF, and then click on the PDF. From there, underline, highlight, or add notes.
Sometimes articles may be retracted, corrected, or otherwise flagged after publication. EndNote does not have any mechanisms for alerting you if papers in your library have been retracted. EndNote also does not import this information when you initially download references into your library, so if you add a new reference you won't necessarily know if it has a potential issue. However, you can create a customized PubMed filter that will allow you to collect this additional information when you bring PubMed references into your library. (Note that if papers are retracted or corrected after you have imported them you will not be alerted, even if you used this filter.) The directions for creating a PubMed filter are below:
EndNote + Zotero
The citation manager Zotero alerts users to retractions via an integration with Retraction Watch. EndNote users can use the two citation managers together to check for retractions. To do this, download and install the Zotero software. When you're ready to check for retractions, export your EndNote references as an ris file and then import that file into Zotero. If you have any retracted references in your file Zotero will immediately alert you.