In the Output Style you are using, you can copy the Bibliography Templates into the Footnotes Templates (one at a time), then (in version X2 at least), there is a check box in the footnotes template that says “Include citations in Bibliography” - uncheck this. Then choose “using footnote format” in the “format citations in” pull down menu. (In older versions of EndNote you may need to delete all the Bibliography templates.)
Hope this helps.