It sounds like Leanpub is probably not the right answer for the next step in your process. If a book manuscript is written in plain text using our markup language, Markua (here's the manual: https://leanpub.com/markua/read), then all you need to do is click a button on Leanpub, and everything will be properly formatted in PDF, EPUB, and MOBI. This process is particularly attractive for authors publishing their books in-progress, chapter-by-chapter.
If your manuscript is finished and you want to get it professionally formatted, you should probably use another service. Then, when the book is done, you can use our "Bring Your Own Book" process to upload your book to Leanpub (in PDF, EPUB, or MOBI format) and sell it on our bookstore and get 80% royalties, if you want to do that. Here is a walkthrough of the process, if you're interested: