Yes, you can include seperate files when needed. But when the code is minified in one. If you use the same file for every page of your application, there will be few requests and the the CSS file and JS file will be cached.
I advise this article which recaps the Asset Pipeline feature: http://coderberry.me/blog/2012/04/24/asset-pipeline-for-dummies/
Q: How can I precompile additional assets without having to include them in the manifest?
Generally in a website, the HTTP request is more longest than reading process the code.
After if you’re not sure you can benchmark your application to see what solution is the best.