The Table of Contents is automatically generated based on the chapters in the book. More correctly, it's based on the parts, chapters, sections, sub-sections, sub-sub-sections, etc.

Here is a section from the Markua manual that shows how to create sub-sections in your book:

https://leanpub.com/markua/read#leanpub-auto-how-to-write-a-computer-programming-book-in-markua

(These instructions apply to all books, not just computer programming books!)

With your Book Theme settings, can choose whether to number your parts, chapters, and sub-sections, and whether to use dots, in your Table of Contents.
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The way you enable numbering (e.g. 1, 1.1, etc) is in the "Section Numbering" section of a Custom theme. This is also where you choose whether to number parts, and whether the table of contents uses dots between the chapter or section name and the page number.
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Please note that custom themes are part of Standard and Pro plans. Here is an article about our Book Themes: http://help.leanpub.com/en/articles/3691789-what-are-the-settings-for-each-of-the-different-book-themes.
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Your plan can be edited at https://leanpub.com/author_dashboard/subscriptions.

Author subscriptions help pay for us to provide support, and one of the things that requires support is the custom Themes, so we feel this is appropriate...