Many non-fiction books utilize footnotes or endnotes. Footnotes do not work very well with ebooks because footnotes need to be placed at the bottom of a page. It is possible with EPUB to specify content to be shown at the bottom of a page using the following:
<div style="display: oeb-page-foot">...</div>
I highly recommend against using the oeb-page-foot display style. Many reading devices and software do not support this and just ignore this text. My recommendation is to use endnotes.
All endnotes should be collected into a single page located at the end of the ebook. I recommend using either a * or increasing numbers. If you use numbers the number in the text should correspond and be displayed infront of the endnote. Use the sup tag and link to the end note.
<sup id="ra"><a href="c2.xhtml#enda">*</a></sup>
One thing to keep in mind is not all ebook reading device and software support a back button. So it’s a good idea to include a return link to take the reader back to the exact place in the text the endnote is referenced by. Make the return link subtle but not something the reader will over look. I just make the font smaller.
<sub><a class="return" href="c1.xhtml#ra">return</a></sub>
The best way to illustrate this concept is with an example. Download ft-endnotes.epub. Opening the file with Sigil you will see the example chapters and the external CSS that is referenced by each XHTML file.