This is what a functional footnote looks like in one of my books. The footnotes are part of the chapter itself and not a separate file. Tapping on the asterisk in the body text will open the footnote pop-up window, and tapping on the asterisk next to the footnote will jump to the page that references the footnote.
Code:
<a class="hlink" href="#c03-ftn3" id="c03-ftn3a"><sup class="frac">*</sup></a>
<p class="footnote" id="c03-ftn3"><a class="hlink" href="#c03-ftn3a">*</a>Shiny footnote text</p>