In a printed text, the most common treatment for footnotes is to put them at the end of the page to which they refer. Sometimes, editors gather them all at the end of the book. Footnotes are a real formatting problem for an eBook without defined physical pages; there is no agreement between readers about which is the best way to render them.
There are three basic ways of rendering footnotes in an e-text:
You can insert them right into the text, in brackets, at the point in the paragraph where they occur, with or without an indication that they were originally footnotes. This is only reasonable in a text with very short footnotes.
You can insert them after the paragraph to which they refer, either contiguous with the paragraph or as a new "paragraph" of their own, as I am doing with this one. If the text contains any footnotes longer than a line,  you should not try to just append them to the paragraph; you should make a new "paragraph" of them, with a blank line before and after.
 Some footnotes can go on not only for several lines, but for several pages!
You can gather all footnotes at the end of the e-text, or to the end of the chapter to which they refer.
Of these three, gathering all footnotes to the end of the chapter or the end of the whole text is probably the friendliest option, since it preserves the original intention of allowing the reader to continue reading the main text without interruption. However, it may involve some renumbering and general note-keeping on your part, and may not be needed where there are only a few short footnotes. You can see an ideal example of this kind of footnote marking in our edition of Darwin's "The Voyage of the Beagle", file vbgle10.txt from 1997, Etext number 944, which you can get from: <ftp://ftp.ibiblio.org/pub/docs/books/gutenberg/etext97/vbgle10.txt>