Ask pynch. He's the footnote champion.
What I did with the two I've epubified so far is just running a search and replace, replacing
with
and put
Code:
.small {font-size: 0.8em}
in the stylesheet. That works fine for me - makes the footnotes smaller, setting them off from the text, and keeps them where they are, which is close enough to their anchor in the text to get there and back with one or two page turns.
That's good enough for me until I find one that I really want to turn into a beauty.