those tags are helpers, so they point to the asset folder and respectively the folder /javascripts or /stylesheets.
<%= javascript_include_tag "something" %>
generates a link to /assets/javascripts/something.js
You can edit the path in config/application.rb just place
config.assets.enabled = true
config.assets.paths << "#{Rails.root}/app/or_whatever_path_to_use"
in there