The Book.txt file just puts the files in order. (You could write an entire Leanpub book in one file, and then Book.txt would just list that file name.) The content of the files determines the chapters, sections, etc. If you type
# Title at the beginning of a line
it becomes an H1 which is a chapter. Everything after that will be in that chapter until the next
# Title at the beginning of a line
which will start the next chapter.