The simplest is [square brackets and identifier] Don't use a superscript like paper or people can't tap on it. Make sure each footnote is only used once and has the link back to the paragraph start. Anchors are best at the start of a paragraph. Then stick all the footnotes at the end under a suitable heading.
There is a FANCIER way, but not everything supports it. I don't especially produce kepub as that's purely an artificial Kobo format. What I've described will work in old mobi, azw/kf8, KFX, epub2, kepub and epub3. Probably in any format and any ereader that supports user links in the text.
So in summary I'd only distinguish the regular link and footnote by:
- Style of the source link, at least putting [ and ] around it. Make sure it's big enough to tap, not like a paper book[3] as superscript, maybe [-3-]. The underlining is of course automatic.
- Each footnote referred to once. If it's needed more often then repeat it as it must link back to source paragraph
- Make entire footnote a link back to anchor at source paragraph OR end with the text [^BACK]
- Put them all together as "endnotes" under a suitable heading at the end.