It's a team matter. The way your team feels comfortable to collaborate, it's the way it should be. And of course if you're using BEM o SMACSS you'll organize your css according to it. I use SASS as my css preprocessor and I have always 3 main folders:
Each of them has a *_{foldername}.scss* and so on, that import the files of this folder that I will use; in that way in my main.scss or style.scss I only have to import one file per folder. And in the root "styles" folder a always has a _fix.scss when I'm using a framework, so I can put simple "Fixes" in it.
The way i write my css is as @xirclebox said: from top to bottom in order as the elements appear on my html, so I can navigate in my styles and HTML in the same way.
PD: Apologies for my english :D