Working with 2 libraries


I work on 2 research papers in MS Word, each having its own separate Endnote library. I dont want to create groups or merge these libraries. 

The papers do not appear to stay linked to each own libraries, instead, when I open MS Word and try to update the references, and Endnote opens, it opens the library which I worked with last, but not the library associated with the paper. 

How can I make sure that the Word documents remain connected to their own libraries?

Thank you!