The Prefix and Suffix boxes won’t work at all with footnote styles. The only “edit citation” function available with footnote styles is the Pages box.
In theory, you write your footnotes (however long) as normal, and just insert the references at the appropriate places.
The problem is that most of the footnote styles supplied with EndNote are formatted to produce a period at the end of the reference. That’s fine if the reference comes at the end of a sentence in your footnote, but doesn’t work well otherwise.
You can amend the output styles to remove the periods at the end of the references in the footnotes (using the Footnote>Templates section of the style). This seems sensible, but it can cause a few odd problems with repeated citations (ibids, and short titles).
Experienced users of footnote styles may have some better thoughts on this.