I've recently tried using sphinx-apidoc from Sphinx to help generate Sphinx specific reStructuredText from the API of a Python project.
However, the result I'm getting is:
Anyone know if I can customize the template
The sphinx-apidoc script uses the apidoc.py module. I am not able to provide detailed instructions, but in order to remove headings or otherwise customize the output, you'll have to write your own version of this module. There is no other "template".
Note that if the API and module structure is stable, there is no need to run sphinx-apidoc repeatedly. You can post-process the generated rst files to your liking once and then place them under version control. See also http://stackoverflow.com/a/28481785/407651.