There are currently four documents we call "manuals". Here they are, with brief descriptions:
The Leanpub Manual
This manual is a great resource if you're getting started on Leanpub with your first book, or you're trying out a new writing mode.
The Markua Manual
If you want to write a Leanpub book in plain text, you'll be writing in Markua. Markua is based on CommonMark, which is the best specification of Markdown, and adds a number of extensions for books and courses. The Markua Manual documents the beta version of Markua which is used in Leanpub today. If you want to see the spec for Markua (which is ahead of the Leanpub implementation), it's at http://markua.com.
The Leanpub-Flavoured Markdown Manual
This is the manual for old-school Leanpub authors who are writing their books in Leanpub-Flavoured Markdown.
The Old Leanpub Manual
This is the old manual. It is for really old-school Leanpub authors who miss the old manual. Note that this manual is outdated, and the screenshots in it are especially outdated. However, if you were used to this manual and want to read it, here it is.