Although EndNote can format papers using references from more than one library, we do not recommend that you use multiple libraries when writing a paper. Keeping all of your references together in one library simplifies the writing process because you know exactly where to find each reference, and you only need to have the one library open when formatting.
If you are collaborating with other authors on a document, however, using multiple libraries for a paper may be a useful and necessary thing to do. You likely will want to use the "Merge Duplicates in Bibliography" preference under Formatting Preferences if you plan to insert citations from more than one library into a paper.
Note: If citations have been inserted into one document from multiple libraries, all of the necessary libraries must be opened in order for EndNote to format the paper correctly.