This is the same thing as footnotes.
At present, the best way of doing this is with bi-directional links.
As an example:
Main text:
Code:
<p>‘No, I won’t cast a stone,’<sup><a id="part01ch22ren33"/><a href="notes.html#part01ch22en33">33</a></sup> she replied to something, [...]</p>
Notes.html:
Code:
<p class="noindent"><a id="part01ch22en33"/><strong><a href="part01chapter22.html#part01ch22ren33">33</a> cast a stone:</strong> ‘He that is without sin among you, let him first cast a stone at her’ (John 8:7).</p>
If your citations are set as footnotes in a Word doc, then Atlantis will automatically encode the necessary links when it makes the conversion to epub, one of the reasons I recommend it for those who don't want to sit up to 3am hand-coding epubs.