don't use it, cause it is under development.
you need to add a config file (json) under your project's root directory, like this one:
https://github.com/shi-yan/Swiftly/blob/master/doctory.conf
to specify the folder of your project that contains the doxygen config file.
readthedocs + breathe might be the best right now.
I have seen someone making really good looking doxygen skins, like this
http://doc.magnum.graphics/magnum/namespaceMagnum_1_1GL.html...
but I don't know if it is opensource.