[eschwartz]

As Kovid said, use as the input file, the opf which lists all the book's resources.

But maybe you should be using the editor? If you are tweaking, you may not want some of the changes a conversion will do. Like flattening the CSS, which is only nice for end users that just want the book on their device already.

The editor will pop open the book and offer you the raw resources, with lots of useful tools to process them and a checkpoint system for reverting mistakes. Or use the Unpack book feature to temporarily extract the book to a temp folder, where you can edit it with any tools you might prefer before rebuilding it.