To edit JavaScript embedded in HTML or JSP create a project that supports JSP or HTML. JSDT Requires no additional configuration for WST based projects that support HTML or JSP. (Unless the project was created before the JSDT was installed.
Below are instructions for a Static Web Project (HTML + JavaScript) but many other project types will work.
Select File --> New--> Project
Expand the Web folder and choose Static Web Project from the New Project Wizard Dialog
Type a project name in the Project name field and click Finish