Good question. I know this is possible in the Eclipse IDE via the Checkstyle plugin's GUI. But in IntelliJ, the GUI can't seem to do that. So you'll probably end up filing a feature request with the Checkstyle-IDEA folks. Until it gets implemented, here are two workarounds:
You could put your test classes into a separate "test project". This is something I'd really hate to do, actually wouldn't want to, especially if you already have a large number of projects to begin with.
A better workaround might be to use IntelliJ's inspections, which are also very powerful and may cover the cases where you need rules to differ. Inspections can be applied to scopes (e.g. only to tests), which is just what you need.
Then you would use Checkstyle for everything that is the same across the entire project, and use IntelliJ's inspections for checks that you only want to perform on a smaller scope.