How can I put footnotes in an ebook?

There's no easy and global solution to it. I'd recommend using some kind of side-notes as described here.

Note that if your target is mainly EPUB3, you can create popfootnotes as described here.

I don't think there is an official way to put footnotes, at least in EPUB2. What I do in the ebooks I prepare is to add an hyperlink to the note (placed in a chapter of its own at the end of the book, and to put at the end of the note another hyperlink which goes back to the original position. It's a bit ugly, but at least it helps readers (in the sense of people, not devices!)

If you only are afraid of your users reading the other footnotes if they are displayed as endnoted, then it might suffice to put each of them on their own page.

If you include an explicit back-link to the original location for the footnote at the end of the footnote ([continue reading ...]) as well, the reader is more likely to get back to the position they came from to read the foot-/end-note.

If you're producing PDFs, their physical layout will be honored to a degree, then you can just use a PDF production tool which understands footnotes.

PrinceXML has high quality footnote support, as well as a styling language you already know (radically modern CSS3,) as well as basically everything else you would ever dare to want, as well as a startlingly active forum where users give compellingly weird solutions to really complex problems. However, it's rather expensive - five hundred, last I looked. (I love it, so I bought it.)

There is a free similar tool called WEasyPrint, but since I had Prince before WEasyPrint existed, I haven't had any reason to switch, and as such I cannot speak to its quality. I hear good things.

Here is Amazon documentation on footnotes editing

Here is how to create footnotes in HTML:

Amazon strongly recommends marking footnotes with the HTML5 aside element, together with the epub:type attribute. This allows accessible reading systems to ignore the footnotes except when followed by their referents and allows any reading system to handle them more intelligently (e.g., as popups). This usage ensures that even if the EPUB semantic is not recognized, the notes will still be treated as secondary content due the nature of the HTML5 aside element.

Regardless of whether the aside element is used, Amazon requires formatting footnotes with bidirectional hyperlinks (the text is linked to the footnote and the footnote is linked back to the text). This makes it easier for customers to return to the text after viewing the footnote. On some Kindle devices, such as Kindle Paperwhite, footnotes with bi-directional hyperlinks are displayed in a pop-up.

For a better reading experience, Amazon strongly recommends placing the footnote text at the end of the chapter or book

This is one of the simplest ways to create linked footnotes using HTML, but there are many others. Please note that Amazon requires footnote links to be superscript.

Place this HTML code in your main body content where you want the footnote link to appear:

<p>This footnote example uses the aside element with the epub:type attribute and bi-directional hyperlinks.<sup><a id="source" href="#ft-1-1" epub:type="noteref">1</a></sup></p>

...

<aside id="ft-1-1" epub:type="footnote">

<p><a epub:type="noteref" href="#source">1.</a> This is the footnote text, which should be placed at the end of the chapter or book.</p>

</aside> 

Change the number value for each footnote that you include in your text. The first footnote in your book should use the number 1, the second footnote should use 2, the third should use 3, and so on:

And describe your footnote:

<p id="footnote-1" epub:type="footnote">Here is the footnote text</p>

After you've set all your footnotes, they'll be converted to endnotes automatically when you upload your book

Sometimes it will open as a popup, but sometimes the navigation will take you to the page. I don't know exactly why. It looks like there's some heuristics involved.

Try always to put your footnotes in another section and have the link superscripted. You can find more tips on this page.

Here is some documentation of special tags and attributes.