Not only is Scrivener more stable and less intrusive for writing than Word, but it has built-in organizing and bookshelf capabilities that help me collect necessary background information, get my thoughts sorted, and chapterize and reorganize things as makes sense. It's easy on the eyes and very thoughtfully put-together-- obviously a tool constructed by a writer for writers. And, once my draft is done, it exports to Word and other formats beautifully, so editors or colleagues don't need to use Scrivener also. (However, it's available for Windows now, so those editors-and-colleagues are missing a treat if they don't. Even Linux users can get in on the fun.)
One thing Scrivener (and Word) is missing is slick citation and bibliography management. Scrivener natively supports EndNote, a Thomson Reuters bibliography-management package. But that solution costs several times what Scrivener itself does. I'm sure it's a very powerful solution, but for me it's overkill.
By comparison, Zotero is a free, cross-platform, open-source, cloud-enhanced "personal research assistant" that performs critical citation management and bibliography functions. I've used it off and on for years, but until recently it supported only the Firefox browser. I much prefer Safari (yay, Reader mode! yay, ctrl-shift-I to email an article!), so it was with delight that I discovered Zotero is now available as a stand-alone app and supports Safari via an extension. http://www.zotero.org/support/3.0 has all the download options; scroll down for the Zotero Standalone app and the Connector extensions for Safari and Chrome.
So here's a straightforward workflow to start with. (Click the photos for a closer view.)
1) Gather your research.Start with Zotero open. Select (highlight) the folder into which you want your citations collected. In Safari, browse to source articles.
Most scholarly publications (and many others, including web pages) are automatically supported by Zotero. You'll see the Zotero button to the left of the omnibar turn from to to indicate the article is capture-able by Zotero. Click it, and the citation will automatically be added to your folder in Zotero.
2) Add your source items to your Scrivener project for offline access.Now drag the little icon next to the URL in Safari's omnibar into your Scrivener project.
...Now you have the citation information in Zotero and the source item in your Scrivener project binder. (If it's a web page, it'll be stored fully rendered-- absolutely marvelous for making productive use of airborne hours.) As you write, ctrl-opt-F lets you search your entire project for keywords-- a boon.
3) Write.What I've been doing is spewing words onto the draft, and when comes time to insert a citation I just type two brackets  and then drag the citation into them from Zotero:
Then, select the citation and make it into an inline footnote:
The citation remains readable to me as I write:
...but it will turn into a footnote when I export (compile) it to send to an editor or colleague:
Here's what it looks like in Word:
You can get much fancier. If, for example, you need to submit your manuscript to several places which might mandate different citation formats, blogger Liz at Confectious.net has documented a very slick way of putting textual cites in your manuscript in curly braces and then having Zotero scan, format and output your work with the necessary citation format.