Yes, you can have multiple CSS files. Put them in your app directories, and you can reference them in your dashboards. Simple XML dashboards in Splunk 6 load dashboard.js and dashboard.css by default. (In older versions, the default files were application.js and application.css.)
Here is some documentation about CSS files in Splunk and where they should be stored. In your dashboard XML (first line), you need to reference the custom CSS file:
<dashboard stylesheet="myCustomFile.css">
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