Just add the links and anchors and see what happens. Footnotes on the Kobo's are just links to the note. With epubs, the link navigates to the location and you use use the previous location button to get back to where you were.
For kepubs, the device uses heuristics to decide if a link is a footnote or not. If it looks like a footnote, the text will be displayed in a pop-up. If the notes are formatted separately, the links will probably be interpreted correctly. You can use the epub3 ePub:type identifying attribute if the kepub is also epub 3.
Kobo has some information about footnotes in kepubs at
https://github.com/kobolabs/epub-spe...kobo-platforms.