I've yet to figure out a method which will work 100% of the time for responsive CSS. There are several different reasons why.
Most of the time I put the responsive CSS at the bottom of a file. This helps preserve the cascade.
Sometimes it helps to see CSS in a relevant context. Putting the responsive CSS in the middle of the file preserves context. I rarely do this because one has to search through the entire file to see everything which happens responsively to that item.
Occasionally it makes more sense to put CSS in a template-specific or page-specific file rather than dozens of component stylesheets. There can be too much going on to easily troubleshoot CSS through dozens of files instead of from one centralized location.
Depending on your app it could be argued that one should use resolution specific stylesheets. That is to say "when your website is being viewed on this device, here are ALL of the things which happen differently". I don't do that unless the app has very few pages and needs to support a plethora of device specific conditions.