Hi Fred,
The main document that you need to read is: http://docs.moodle.org/dev/Course_formats - then I suggest looking at the code in core and contributed formats.
From your question perspective, the lib.php file deals with the settings, so you can do something clever there and the renderer.php file deals with the output of the html, specifically starting with the print multiple and one section page methods.
I did a slightly altered topic based format for the University of Waiariki where they wanted slightly different navigation. You can see the code here: https://github.com/gjb2048/moodle-format_waiariki and get an idea of adapted course formats. My GitHub account also contains the code for the other contributed formats: Collapsed Topics, Grid, Columns and Noticeboard - all in one place to browse.
Cheers,
Gareth