To get the script tag to show up, you will have to go to Dreamweaver Preferences and click on the invisible elements section. Make sure the checkbox next to scripts is checked. Then you will have to see the menu in either split or design view and the yellow script tag should be next to the menu. Then you should click on that script tag and in the properties inspector there should be buttons to allow you to edit.
What were the issues that the menu was having when you applied it the first time?