Technically there are two documents where you can embed your CSS/JS files:
Note that you can include CSS/JS into these two documents, but not to result content. Final HTML will be saved without links to these JS/CSS files.
If you use inline editing, editor document and global document are the same.
By default JS+ CKEditor & TinyMCE Include CSS/JS adds specified CSS or JS URLs into web editor document.
If you want to use the CSS/JS for both global and editor document at the same time please use
truethe specified CSS files will be added into global document (whole page with the editor) too.
For knowing more about the process of including Bootstrap or Foundation into your pages please see Bootstrap/Foundation include manual.