I am using \'Read the Docs\' Sphinx theme for my documentation. In the original theme, given below
http://read-the-docs.readthedocs.org/en/latest/theme.html
I would modify this in the css. You should search for the file theme.css (it is in the read-the-doc sources at "sphinx_rtd_theme/static/css/theme.css").
Make a copy of that file and put it in your sphinx _static dir. In that css file you can make all the layout changes that you need. (You might have to read a bit on css files if you have never worked with that.)
Hope this helps.