There's no tool in Calibre to create footnotes/endnotes. You'll have to do it manually. This is what I do for my footnotes:
For the source of the footnote (the place in the text that's pointing at the actual note), I use:
Code:
<a id="fn1" href="#fn1a" epub:type="noteref"><sup>n</sup></a>
That goes right next to the text that you want to have a footnote on. If you're not using epub3, the 'epub:type="noteref"' bit won't work, so just leave it off. Basically, all that does is set up an id on an anchor (the a id="fn1" bit (each footnote will need its own id so the footnote can link back to this location) and link to where the footnote is (the href= bit (again, unique ids, I just tack on an "a" to the end of the anchor id -- if the footnote is in the same file (chapter), then you can get by with the "#" -- if it's in a different file (perhaps an Endnote file near the end of the book), you'll need to insert the actual file name in there -- Calibre should give suggestions as you type).
For the target note, I use:
Code:
<aside id="fn1a" class="footnote" epub:type="footnote"><p><a href="#fn1"><sup>n</sup></a>.thenote.</p></aside>
Epub3 is needed for the aside and the epub:type= bits. If you're using epub2, then ignore the epub:type bit and use a div in place of the aside. The id will be the one the href in the source targeted and the href will use the href back to the source id.
EDIT: Oops. Forgot to mention, the 'class="footnote"' is for whatever css class you set up to format the footnote the way you want it. And, if you are using epub3, the epub:type should be "endnote", not "footnote" if that's what you're setting up.