Here is the section of the Markua manual with instructions for making footnotes:
https://leanpub.com/markua/read#leanpub-auto-footnotes-and-endnotes
Here's an example of how to do it:
# Chapter One
This has a footnote[^footnote].
[^footnote]: This is the footnote.
This will produce the following result (this example is from a PDF version):
In the PDF, the footnote text ("This is the footnote" in the example above) appears at the bottom of the page where you would see the footnote number in the sentence in the main body of the text. In EPUB and MOBI, it appears at the end of the book, but you can also click the footnote number to "jump" to the footnote, text, and then "jump" back to the main body text.
So, for example, you could type:
[^footnote]: This is the footnote....at the very end of your text file, and it will work properly.
Please note that you don't have to type [^footnote]; this "anchor" can be anything you like, and should be different for each footnote.
Also, no matter what you choose for the "anchors", the footnotes will be numbered sequentially.
For example, you might do:
# Chapter One
This has a footnote[^1]. Here is a second footnote[^2].
[^1]: This is the footnote.
[^2]: This is a second footnote.or:
# Chapter One
This has a footnote[^a]. Here is a second footnote[^b].
[^a]: This is the footnote.
[^b]: This is a second footnote.Just to be clear, the footnote "anchors" are not visible to readers. So, you can use numbers in the footnote "anchors" if you want to, but they will not affect the displayed footnote numbering in the book, which just happens in the order the footnotes appear in your manuscript.
You can see the footnote settings for your book on your book's Theme page here:
leanpub.com/YOUR_BOOK/settings/theme...making sure to replace YOUR_BOOK with your book's unique web address.