application.css and application.js are not regular css and js files (they can be, but they serve a different purpose
both are manifest files that describe the asset pipeline along with asterisks for js
therefore, as Michael Darrant correctly pointed out, http://guides.rubyonrails.org/asset_pipeline.html#manifest-files-and-directives will be the right place
but according to your other questions, it seems that you are missing a pretty critical piece of the puzzle
Rails mainly work with precious stones. Gems are pieces of ruby code that you can tell to add rails to your application through bundler
when you add a gem like a self-tuning gem, it is installed (by default, in the stone library where you have the ruby installed - something like Ruby193 \ lib \ ruby \ gems \ 1.9.1 \ gems)
If you go there and look at the bootstrap gem, you will find the css and js files that are included in the application, as well as the jquery and jquery_ujs that you included in the manifest file
since gems are placed next to the rails, the rails do not mind where the files are (as long as they know where they are).
So, the manifest file tells the rails "Hey, include this file for me in this particular order" That's why you can include the files you wrote that are in the resources folder and the files are included in the gem
If you do not include the files in the manifest, but still install a gem equivalent to writing a css or js file, placing it in some folder and not reporting that it exists. When you tell the rails where it is through the manifest file, it will include it in the asset compilation process, and you can access it regularly.
Alternatively, you do not need to use the asset pipeline for assets
you can include css and js file with normal
<script type="text/javascript" src="//ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js"></script>
and just place the files somewhere and point them to the files, but the resource pipeline has many advantages, and it really makes your life easier when you recognize it.