Short titles are usually imported from a database as such into the “Short Title” field of the record in your library. Endnote simply uses the content of that field in your output as defined in the footnote templates, or the full title if the field is empty.
If they aren’t short enough, or if the field remains empty in the record, I think that you will need to edit each record’s short title, to shorten it, or copy what you want to appear as the short title into each library record that you cite in the footnotes.
remember that if the field is empty, you will need to be displaying all fields, or it will be hidden, when you are in the edit record mode. In the image attached, I show a book with a short title and the full title. I also show where you would “show empty fields” but have that off in this view, so I can capture both fields in the image (otherwise the short title would pushed pretty far down the page by the empty fields).
