The extension .dox is normally used for special pages in doxygen.
You can use the regular doxygen commands found here:
http://www.doxygen.nl/manual/commands.html
Normally, you start a special page via @page or @mainpage.
The template you generated is the configuration for doxygen, there you define how/which output is generated, which files to include and more.
The documentation for the configuration is here:
http://www.doxygen.nl/manual/config.html
So the first is content (pages, like commenting code), the second is toolchain configuration.
You can explicitly configure doxygen to include your .dox file via
INCLUDE += myfile.dox
in your .doxycfg.
Also see these questions on SO: