You just need to format the bibliography and select an output style that does superscript citations. To do this:
In the document, do the following:
Word 2011: Go to the “Tools” Menu and choose "EndNote > Format Bibliography or Bibliogrpahy Settings or Configure Bibliography.
Here, select the Output Style you would like to use in the Output Style dropdown menu. A generic output style you can use for this purpose is the “Account Chemical Res” or “JAMA” or “New England Journal of Medicine” style.
In Word 2011: Click the OK button to format the document using your selected style.