You can cite references from multiple libraries. Simply open the selected libraries before you begin inserting citations.
If possible, though, we recommend that you use a single library when writing a paper. Keeping all of your references in one library simplifies the writing process because you know exactly where to find each reference, there is little likelihood of duplicate references, and you only need to have one library open when inserting citations.
Note: If you plan to insert citations from more than one library into a paper, read about the Merge Duplicates in Bibliography preference