In order to change a numbered style to use superscript numbers you must first follow the instructions for ‘style editing and saving’ from
http://www.ncl.ac.uk/library/endnote_tips_style.php

Once you have saved the style you wish to edit onto your file space, you should select:
>Edit
>Output styles
>Edit (style name of your choice)
Under the citations heading select
>templates
Highlight ‘Bibliography number’ and hold down the Ctrl and shift keys and select +, this will superscript the bibliography number in in-text citations when using this style. You can also delete any brackets which appear around the bibliography number from here too.