[enuddleyarbl]

The little I've seen on AZW3 and footnotes implies the footnotes should be two-way linked and use

<a>, <aside>, epub:type="noteref", and epub:type="footnote"

. I don't know how much credence to put in that, though.

Try formatting the call to the footnote in the text as:

<a id="fn1" href="#fn1a" epub:type="noteref"><sup>n</sup></a>...</p>

and format the footnote with:

<aside id="fn1a" class="footnote" epub:type="footnote"><p><a href="#fn1"><sup>n</sup></a>.thenote.</p></aside>

Replace the various ids, the footnote number, and the "class="footnote"" bit with whatever you want. Here's what I use for the "footnote" class:

.footnote {
/* Footnote Styling */
  font-family: sans-serif;
  font-size: small;
  padding-top: 0.1em;
  padding-bottom: 0.1em;
  margin-left: 4em;
  margin-right: 4em;
  text-indent: 0;
  border-top: 1px solid black;
  border-bottom: 1px solid black;
  page-break-inside: avoid;
}

I put my footnotes immediately following the paragraph that calls them. But, even with EPUB3 on my Kobo, I don't necessarily get a popup. But, at least if the popup fails, the footnote is nearby.