Jekyll bower's main goal is to easily integrate bower installed components into your jekyll website.
place the jekyll-bower.rb file inside the _plugins folder in your Jekylls site root directory. Now, everytime jekyll builds your site. bower dependencies will be copied to the assets folder.
NOTE only files listed as main in each bower packages bower.json will be copied. Directory structure left intact.
In order for Jekyll to ignore bowers default installation directory. Add bower_components to the exclude list in your _config.yml file. More details on how to do that, here documentation.