How to use EndNote in a thesis with multiple chapters?

I am finalizing my PhD Thesis which I wrote as three independent journal articles using EndNote X5. When I merge the documents, all text below the original bibliography becomes hightlighted when selected, as if it is being treated as part of the bibliography. How can I have multiple bibliographies within the text of my thesis and not have them affect the formatting of the rest of the thesis? Any suggestions would be greatly appreciated. Thank you!

Create the base document, put in the section breaks, and then put your individual chapters in each section.  - To keep things straight and to ensure you aren’t including partial fields, you could first unformat your chapters so they in curly bracketed form.  You want to make sure you are using an output style which is set up to include the bibliography per section.  (that is assuming you want individual bibliographies).