You can configure the generation of the output from a ditamap. Using the ditafm-output.ini file (at %appdata%\Adobe\FrameMaker\<Version Number>), you can configure the various options for your output, such as:
Type of output to generate (book with FM components or compound FM document)
Templates to use for chapter, section, subsection ToC, index, and front matter in the generated book
Chapter numbers, pagination, para numbers, footnotes, and table footnote numbers