It's been awhile since I've messed with MediaWiki, so it's possible things have changed. But, IIRC, you just need to create the page "MediaWiki:Common.css" and save your custom styling to it. MediaWiki should import it on its own.
Apologies for possibly de-railing this topic as I can't answer your question, but I do feel obligated to warn you about getting in too deep with MediaWiki. It is very difficult to manage or customize, and became a significant administrative burden for me and my staff during the four years or so I used it as part of my site.
Having said that, if you can't get help here and do continue working with MediaWiki, you may find this forum helpful (despite the fact they're using vB 4 and not XenForo!).
Interesting... I've had a much better experience with MediaWiki. It requires contributors to use Wikitext (like BBCode, but more powerful and complicated), which I find users are becoming less tolerant of. However, contributing to a wiki is a significant commitment anyway. One needs to learn about conflict resolution and other norms of the community if one is going to participate in the group writing project. In that sense, the technical hurdle of the wikitext might be a good screening tool.
The forum mentioned above, mwusers, is a little dead, though. I find that more responsive support from developers, etc., can be had from the mediawiki-l list sponsored by the Wikimedia Foundation. It's archives can be searched on gossamer threads.
I think Common.css gets loaded on its own. Just Google it.
The wiki I contribute to and administrate can be found at http://www.tmswiki.org/ . It's a little rough, still, because all of the pages were brought over from an archive by a PHP script that had to translate from the HTML to the wikitext. Since the HTML was human modified (from a Wetpaint wiki), this did not go smoothly.