Integration with automake
First copy the Makefile.am from the examples subdirectory of the GTK-Doc sources to your project's API documentation directory (./docs/reference/package). If you have multiple doc-packages, repeat this for each one.
The next step is to edit the settings inside the Makefile.am. All the settings have a comment above that describes their purpose. Most settings are extra flags passed to the respective tools. Every tool has a variable of the form <TOOLNAME>_OPTIONS. All the tools support --help to list the supported parameters.
You may also want to enable GTK-Doc for the distcheck make target. Just add the one line shown in the next example to your top-level Makefile.am:
DISTCHECK_CONFIGURE_FLAGS=--enable-gtk-doc