In Word 2007, first press Ctrl+Shift+S to display the Apply Styles floating
dialog. Select the footnote's number or symbol, the one that should be
superscript. In the dropdown of the Apply Styles dialog you should see "Footnote
Reference", which is the name of the style that's automatically applied to the
footnote number. Click the Modify button.
In the Modify Style dialog that appears, select the "New documents based on this
template" option. Then click the Format button at the bottom left of the dialog
and choose Font. In the Font dialog that appears next, check the Superscript
option, leave everything else unchanged, and click OK in each dialog.