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Not sure if there is one right way to handle footnotes. In paper books you'll also find them at the end of the page, at the end of the chapter or in a separate section at the end of the book.
With ebooks it might be the same. My personal preference:
- if the book has few short footnotes, they may be placed at the end of a paragraph as mentioned by DaleDe,
- if they are a bit longer but there are not too many per chapter, I'd put them at the end of the chapter, if they are still not disruptive to the reading
- many footnotes or very long footnotes: I'd put them at the end of the book
In the last 2 cases, linking to the footnote and back to the text are a must.
But that is just my preference, I have seen from other dicussions that quite a few people have different preferences.
It's the same with many of the other formatting issues which are frequently discussed around here (indent or extra space to mark a new paragraph, serif or not, font size, ...).
So feel free to do what you like best, some people will like it and some will not.
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