You have to insert it in the proper *.inc in the "country" section.
For an example of how this is used, go to the \scenarios\1936 folder and open the "japan.inc" file and search the document for "nationalidentity", that should jump you to where the national ideas are defined for Japan in the 1936 scenario. What you insert must match the idea's personality_string as defined in its entry in "ideas.txt". Obviously, you can add/remove/modify national idea effects at your leisure.
P.S. : Technically,these kinds of questions would belong in the "User Modifications" section. Just for future reference.