android.moparisthebest.org/source/docs/deploying/_subdir.markdown

If you're deploying to a subdirectory on your site, or if you're using Github's project pages, make sure you set up your urls correctly in your configs. You can do this almost automatically:

    rake set_root_dir[your/path]

    # To go back to publishing to the document root
    rake set_root_dir[/]

Then update your _config.yml and Rakefile as follows:

    # _config.yml
    url: http://yoursite.com/your/path

    # Rakefile (if deploying with rsync)
    document_root = "~/yoursite.com/your/path"

To manually configure deployment to a subdirectory, you'll change _config.yml, config.rb and Rakefile. Here's an example for deploying the Octopress website to Github Project Pages:

    # _config.yml
    destination: public/octopress
    url: http://imathis.github.com/octopress
    subscribe_rss: /octopress/atom.xml
    root: /octopress

    # config.rb - for Compass & Sass
    http_path = "/octopress"
    http_images_path = "/octopress/images"
    http_fonts_path = "/octopress/fonts"
    css_dir = "public/octopress/stylesheets"

    # Rakefile
    public_dir = "public/octopress"
    # If deploying with rsync, update your Rakefile path
    document_root = "~/yoursite.com/your/path"