Normally jekyll will put the css file in the _site/assets folder.
But you should be able to ignore that when you edit the sass files in _sass. It will simply be included where needed for you.
To make this clear:
1) You should edit the SASS files in _sass/... (and do all your CSS as SASS in there)
2) You should not manually include a css file in a posting or page.
Once you compile your site, the CSS will appear in _site/assets/main.css and this file will be included by the header that is also generated by jekyll.
Use this trick: point your browser at _site/index.html and switch to "show page source". (Or use a plain old text editor). Then take a look at the HTML code that was generated.This way I found out fairly quick how jekyll works, even for those things that are difficult to find in the documentation.