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I tend to use multiple CSS files, but not for the same purpose that you do. I have one CSS file that controls the site wide styles, such as basic header and paragraph styles as well as page backgrounds, and outer containers. Then I have another CSS file that is for content and is for the most part specific to individual pages or templates. In addition to those two, I have two more CSS files that specifically target IE6 and IE7.

One recommendation i can give you is to use ‘flags’ as recommended by Doug Bowman http://stopdesign.com/log/2005/05/03/css-tip-flags.html. The basic idea is to use comments that have a character that won’t be used anywhere else in the CSS and he uses the =. Here’s an example:

So when you search for =header it will take you right there.

Another option — and one that I use — is CSSEdit’s groups. It adds some semantic comments to your CSS that allow CSSEdit to group all of your styles neatly in its sidebar.