The code that is on the page for you menu should not be duplicated in any way when you edit the them. The code that is on the page should be CSS references, the js file, then the menu itself or the serverside code for the menu.
Are you doing this on a static html site or a PHP or other server model site? What are the exact steps you are taking that result in this. I can edit the theme for the applied menu by selecting the menu code on the page, then clicking on the edit theme button in the property inspector. I then change some settings and click finish, when I'm prompted to save the preset I do not choose to save and just finish.
Are these the same steps you are taking? Do you have this menu applied to a template that has menu code on it already? Please post back with as much info about this as you can so that we can try to determine what is going on.