What you need to do is compile your manuscript to plain text.
- In your compile options, first select “Plain text” from the top drop-down menu.
- Then select the “Plain Text Manuscript” compile format from the left hand column.
- Click the “Assign Section Layouts” button, and assign your headings, chapters and sections to appropriate formats.
- In the replacements tab of the right-hand pane, create a new replacement. In the first text box, type ctrl-return, and in the second one type ctrl-return twice. It won’t look like anything is there, but trust me, you’ll need this to have visual separation between your paragraphs.
- Run your compile.
This will produce a manuscript with footnote numbers in brackets in the body of your text, and the footnote contents as endnotes, just the way we used to type them manually. 
Hope this helps!
