A KML feature can only contain a single styleUrl with a single style reference but the feature can also contain an inline Style element. This technique is called a "merged" style.
In the case where a feature has both a shared style and inline style, the shared style is applied first then the inline style overrides whatever is already specified in the former.
If you use the BallonStyle as a shared style then you can override specific elements such as color in the inline style.
<Placemark>
<styleUrl>#myBalloonStyle</styleUrl>
<Style>
<LabelStyle>
<color>ff0000cc</color>
</LabelStyle>
</Style>
</Placemark>
Here's a complete example with a global BalloonStyle. Click "Raw", save contents to a local file, then open in Google Earth.