Wwsr,This might work for you. A floating menu bar across the top. As the user scrolls down the page the menu bar remains in position. When the user moves the cursor over an item in the menu bar it expands vertically downward.
This approach allows you to present your navigation several different ways. For example, the first tab could be the chapter listing, the second tab could be a subject listing, the third tab...well, you get the idea.
Also, you might want to make an index so a user could reference your ebook by keyword. And of course there is also the search command.
My philosophy is that different people approach the same material with different experiences. I feel it is imperative to address as many solutions for navigation as possible.